AAA+ proteins:
A family of proteins with ATPase activity that share a common structural domain called the AAA domain, which includes Walker A and Walker B motifs. AAA stands for ATPases associated with diverse cellular activities.
abasic site:
A position in an intact DNA backbone that is missing the base. Also called an AP (apurinic or apyrimidinic) site.
abortive initiation:
Release of an 8 to 10 base pair RNA transcript from the bacterial RNA polymerase initiation complex before it clears the promoter and enters the elongation stage.
accommodation:
A process of checking for appropriate codon-anticodon pairing prior to rotation of an incoming aminoacyl-tRNA into position for peptidyl transfer.
achiral:
Describes a molecule that can be superimposed on its mirror image.
acid dissociation constant (Ka):
The dissociation constant of an acid, HA, describing its dissociation into its conjugate base, A−, and a proton. Ka = [A−][H3O+]/[HA].
acridine:
A planar heterocyclic molecule isolated from coal tar that intercalates between successive G≡C base pairs, deforming the DNA. Acridine inhibits transcription by preventing movement of the RNA polymerase along the DNA template. Acridine is also a mutagen, causing DNA polymerase to insert an extra base during replication.
actinomycin D:
A peptide antibiotic that inhibits transcription elongation by RNA polymerase in bacteria, eukaryotes, and cell extracts. The molecule has a planar heterocyclic region that intercalates between successive G≡C base pairs, deforming the DNA and preventing movement of the RNA polymerase along the template.
activation:
The positive regulation of the expression of a gene or genes.
activation energy (ΔG‡):
The difference in free energy between the ground state of a reacting substance and the transition state.
activator:
(1) A DNA-binding protein that positively regulates the expression of one or more genes; that is, transcription rates increase when an activator is bound to the DNA. (2) A positive modulator of an allosteric enzyme.
active site:
The region of an enzyme surface that binds the substrate molecule and catalytically transforms it. Also called a catalytic site.
ADAR:
See adenosine deaminase acting on RNA.
adenine (A):
A purine base that is a component of DNA and RNA.
adenosine 3′,5′-cyclic monophosphate:
See cyclic AMP.
adenosine deaminase acting on RNA (ADAR):
An enzyme that catalyzes the conversion of adenosine to inosine by removal of the amino group at C-6 on the adenine ring.
adenylylation step:
The first (activation) step in the attachment of an amino acid to a tRNA. The aminoacyl-tRNA synthetase reacts with the α-phosphoryl group of ATP, displacing pyrophosphate and forming a 5′-aminoacyl adenylate intermediate. See also tRNA-charging step.
A-DNA (A-form DNA):
Conformation of double-stranded DNA observed under certain nonaqueous solvent conditions. The molecule assumes a right-handed helix with 11 base pairs per turn and a rise of 2.6 Å per base pair. Compare B-DNA and Z-DNA.
adult stem cells:
The cells in adult mammals that retain the ability to divide and differentiate into other cell types. Compare embryonic stem cells.
affinity chromatography:
A type of column chromatography in which molecules are separated based on their binding affinity for chemical groups present on the stationary phase.
alkylation:
The transfer of an alkyl group from one molecule to another.
allele:
A variant form of a gene at a specific locus.
allopatric speciation:
Geographic isolation of a group of individuals followed by evolution to form a distinct species that no longer can interbreed with the original one.
allosteric enzyme:
A regulatory enzyme with catalytic activity modulated by the noncovalent binding of a specific metabolite at a site other than the active site.
allosteric modulator:
A metabolite that, when bound to the allosteric site of an enzyme, alters its kinetic characteristics.
allosteric protein:
A protein (generally with multiple subunits) with multiple ligand-binding sites, such that ligand binding at one site affects ligand binding at another.
α-amanitin:
A cyclic polypeptide antibiotic that inhibits transcription in eukaryotic cells by binding Pol II and blocking its ability to translocate along the DNA template. At high concentrations it also binds and inhibits Pol III.
α/β barrel:
Common protein domain architecture consisting of eight hydrogen-bonded β strands surrounded by eight α helices. The domain is formed by a series of β-α-β motifs.
α carbon (Cα):
The first carbon atom attached to a functional group. In amino acids, the α carbon is the central carbon to which the amino, carboxyl, and R groups are bonded.
α helix:
A helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen bonding; the most common secondary structure in proteins.
alternative splicing:
The splicing of exons from a single gene in various combinations to produce different mRNAs and thus different polypeptides.
Ames test:
A simple bacterial test for carcinogenicity, based on the assumption that carcinogens are mutagens.
amino acids:
α-Amino–substituted carboxylic acids, the building blocks of proteins.
aminoacyl-tRNA:
An aminoacyl ester of a tRNA; the tRNA is charged with an amino acid.
aminoacyl-tRNA synthetases:
Enzymes that catalyze synthesis of an aminoacyl-tRNA at the expense of ATP energy.
amino terminus (N-terminus):
The end of a polypeptide chain with a free α-amino group.
amphipathic helix:
An α helix with both polar and nonpolar segments.
analyte:
A molecule to be analyzed by mass spectrometry.
anaphase:
The third stage of mitosis (M phase). Sister chromatid pairs held together at the centromere separate, and the two homologous chromosomes move toward opposite spindle poles.
annealing:
Process in which single strands of nucleic acid in solution spontaneously rewind or renature with strands of complementary base sequence to form duplex structures.
anticodon:
A specific sequence of three nucleotides in a tRNA, complementary to a codon for an amino acid in an mRNA.
antiparallel:
Describes two linear polymers that are opposite in polarity or orientation.
antiparallel β sheet:
See β sheet.
AP endonucleases:
Enzymes that cleave the DNA backbone at an AP (apurinic or apyrimidinic; abasic) site as part of the base excision repair pathway.
apoenzyme:
The protein portion of an enzyme, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity.
apoprotein:
The protein portion of a protein, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for activity.
aqueous solution:
Solution in which the solvent is water.
archaea:
One of the three main groups of living organisms. Like bacteria, archaea are unicellular and contain no internal organelles or nucleus; however, archaea are more closely related to eukaryotes with respect to some genes and metabolic pathways. Archaea include many species that thrive in extreme environments of high ionic strength, high temperature, or low pH.
ARE:
See AU-rich element.
A site:
The site in a ribosome where the aminoacyl-tRNA binds.
association constant (Kα):
An equilibrium constant for the association of a complex of two or more biomolecules from its components; for example, association of a substrate with an enzyme. Ka is the reciprocal of the dissociation constant, Kd. Compare dissociation constant (Kd).
atomic orbital:
Mathematical function that describes the behavior of an electron in an atom.
ATP-coupling stoichiometry:
A property of helicases and other motor proteins that describes the number of ATP molecules consumed per distance traveled or other defined work units.
AU-rich element (ARE):
Sequences in mRNA with 5 to 13 residues of A and U, which target the mRNA for rapid degradation.
autoinhibition:
The reduction or elimination of a molecule’s activity by one of its own segments or domains.
autoradiograph:
An image on an x-ray film or on certain photographic plates that is produced by decay emissions of a radioactive substance.
autosome:
Any chromosome that is not a sex chromosome. Compare sex chromosome.
auxotrophic mutant (auxotroph):
A mutant organism defective in the synthesis of a particular biomolecule, which must therefore be supplied for the organism’s growth.
BAC:
See bacterial artificial chromosome.
bacmid:
A large circular DNA that includes the entire baculovirus genome and sequences that allow replication of the bacmid in Escherichia coli; a baculovirus shuttle vector.
bacteria:
One of the three main groups of living organisms; bacteria have a plasma membrane but no internal organelles or nucleus.
bacterial artificial chromosome (BAC):
A plasmid designed as a cloning vector for large segments of DNA. A BAC typically includes cloning sites, one or more selectable markers, and a stable origin of replication.
bacterial transduction:
The transfer of genetic information from one bacterial cell to another by means of a viral vector.
Barr body:
In the cells of female mammals, the inactivated X chromosome, which is compacted into a dense chromatin particle.
basal transcription factor:
In eukaryotic cells, a protein required at every Pol II promoter. Also called a general transcription factor.
base excision repair (BER):
A DNA repair pathway that involves excision of a damaged base by DNA glycosylase, followed by cleavage of the DNA backbone adjacent to the site by an AP endonuclease. Nick translation, DNA polymerization, and ligation complete the repair.
base pair:
Two nucleotides in nucleic acid chains that are paired by hydrogen bonding of their bases; for example, A with T or U, and G with C.
base pairing:
The weak binding of nucleotide bases with each other, via complementary hydrogen bonding, within a nucleic acid with at least two associated strands.
base stacking:
A property of adjacent bases in a DNA strand or of base pairs in a DNA double helix that describes their orientation relative to each other. Parallel orientation of the hydrophobic planar rings minimizes their association with water and contributes to the stability of the B-form (Watson-Crick) double helix. Also called hydrophobic stacking.
basic helix-loop-helix motif:
A protein secondary structural motif typical of transcription activators. It consists of two amphipathic α helices joined by a loop of variable length. Two such motifs dimerize through one pair of α helices. The other α helices have a series of basic amino acid residues along one side through which they bind DNA.
basic leucine zipper motif:
A leucine zipper motif in which one side of the recognition helix has a series of basic residues, which facilitates DNA binding.
B-DNA (B-form DNA):
Standard Watson-Crick conformation of double-stranded DNA. The molecule assumes a right-handed helix with 10.5 nucleotide residues per turn and a rise of 3.4 Å per base pair. Compare A-DNA and Z-DNA.
BER:
See base excision repair.
β-α-β motif:
A protein secondary structural motif in which two parallel β strands are connected by an α helix.
β barrel:
A protein structural domain in which a β sheet of eight or more strands with one hydrophobic surface forms a cylinder in which the first β strand hydrogen-bonds with the last β strand.
β conformation:
An extended conformation of a polypeptide chain, usually stabilized by interchain hydrogen bonding with adjacent polypeptide segments in the same conformation to form a sheet-like structure; the second most common secondary structure in proteins.
β hairpin:
A protein structural motif in which two antiparallel β strands are connected, usually by an α, β, or γ turn.
β sheet:
A common protein secondary structure in which a polypeptide chain assumes an extended, zigzag arrangement with extensive hydrogen bonding between adjacent segments or strands. In parallel β sheets, the strands are aligned with the same polarity. In antiparallel β sheets, adjacent strands have opposite polarity.
β sliding clamp:
A component of the E. coli DNA polymerase III holoenzyme. The ring-shaped homodimer encircles and slides along the duplex DNA ahead of the Pol III core to which it is attached, greatly enhancing the processivity of DNA synthesis.
β turn:
A type of protein secondary structure consisting of four amino acid residues arranged in a tight turn so that the polypeptide turns back on itself.
binding energy (ΔGB):
The energy derived from noncovalent interactions between enzyme and substrate or receptor and ligand.
binding site:
The crevice or pocket on a protein in which a ligand binds.
biochemical standard free-energy change (ΔG′°):
The free-energy change for a reaction occurring under a set of standard conditions: temperature, 298 K; partial pressure of each gas, 1 atm or 101.3 kPa; all solutes at 1 M concentration, pH 7.0, in 55.5 M water.
biological information:
Information required for cellular growth and metabolism, inherited from one generation of an organism to the next. Primarily imprinted within the sequences of nucleic acids, information may also be embedded within nucleic acid modifications and in the patterns of modification in certain proteins bound to nucleic acids; see epigenetic inheritance.
blunt ends:
The product of restriction endonuclease action on double-stranded DNA that leaves no unpaired bases at the cleavage site.
bond angle:
The angle between two adjacent bonds to the same atom.
branch migration:
Movement of the branch point in a branched DNA formed from two DNA molecules with identical sequences. See also Holliday intermediate.
branch point:
An internal A residue just upstream of the 3′ splice site of an intron that attacks the phosphate at the 5′ splice site, forming the loop of the intron lariat.
BRCA1:
A vertebrate protein involved in DNA damage sensing and repair (primarily double-strand break repair). Mutations in the gene encoding BRCA1 confer a predisposition to breast and ovarian cancer.
BRCA2:
A vertebrate recombination mediator protein involved in the repair of double-strand breaks. Mutations in the gene encoding BRCA2 confer a predisposition to breast and ovarian cancer.
bromodomain:
A protein structural domain that recognizes and binds to certain acetylated Lys residues in proteins.
buffering capacity:
Quantitative measure of the ability of a buffer solution to resist changes in pH.
buffer solution:
A system capable of resisting changes in pH, consisting of a conjugate acid-base pair in which the ratio of proton acceptor to proton donor is near unity.
cAMP receptor protein (CRP):
In bacteria, a specific regulatory protein that controls initiation of transcription of the genes that produce the enzymes required for the cell to use some other nutrient when glucose is lacking. Also called catabolite gene activator protein (CAP).
CAP:
See cAMP receptor protein.
cap-binding complex (CBC):
A protein complex that recruits capped mRNAs to the ribosome to initiate translation.
carboxyl terminus (C-terminus):
The end of a polypeptide chain with a free α-carboxyl group.
carcinogen:
A substance directly involved in causing cancer.
catabolite repression:
The inhibition of the expression of genes required for the metabolism of other sugars in the presence of glucose.
catalysis:
An increase in the rate of a chemical reaction caused by a substance that is not consumed by the reaction.
catalyst:
A substance that increases the rate of a chemical reaction without being consumed by the reaction.
catalytic RNA:
See ribozyme.
catenane:
Two or more circular polymeric molecules interlinked by one or more noncovalent topological links, resembling the links of a chain.
CBC:
See cap-binding complex.
cDNA:
See complementary DNA.
cDNA library:
DNA library consisting entirely of cloned cDNAs from a particular organism or cell type.
cell:
Membrane-bounded structure that is the smallest unit of life.
cell cycle:
The process by which cells replicate and divide. The bacterial cell cycle involves binary fission; the eukaryotic cell cycle has four phases, including mitosis.
cell theory:
The theory proposed by Theodor Schwann in 1839 that cells are the basic units of all living things.
cellular function (of a gene product):
The metabolic processes in which a gene product participates and the interactions of that gene product with other proteins or RNAs in the cell. Compare molecular function and phenotypic function.
central dogma:
The organizing principle of molecular biology: genetic information flows from DNA to RNA to protein. The pathways of information flow have been expanded to include RNA to DNA, and RNA to RNA, and are now established. They are no longer constituted dogma.
centromere:
A specialized site in a chromosome, serving as the attachment point for the mitotic or meiotic spindle.
centrosome:
An organelle that serves as the microtubule organizing center. Two centrosomes are responsible for the creation of the spindle apparatus that moves chromosomes to opposite poles of the cell during mitosis and meiosis.
chain topology diagram:
A method of illustrating in two dimensions the topology of the polypeptide chain in supersecondary structures.
change in free energy (ΔG):
See free-energy change (ΔG).
chaperone:
Any protein that interacts with partially folded or improperly folded polypeptides, facilitating the correct folding pathway or providing a microenvironment where proper folding can occur.
chaperonins:
A class of chaperones that form a large, barrel-like structure, inside which certain cellular proteins fold.
Chargaff’s rules:
A set of quantitative observations about the nucleotide content of DNA from many organisms and species that helped to lay the groundwork for the discovery of the structure of DNA.
chemical bond:
An attractive force that holds atoms to each other in a molecule or crystal.
chemical reaction:
A process that changes the structure or energy content of atoms in a molecule, but not their nuclei.
chemical shift:
Variations of nuclear magnetic resonance frequencies, relative to a standard of the same kind of nucleus, caused by variations in the electron distribution within a molecule.
chi:
The sequence 5′-GCTGGTGG-3′, which alters the endonuclease activity of bound RecC in the RecBCD complex so that it preferentially degrades the 5′ end of the molecule.
chiasma (pl. chiasmata):
A cross-shaped junction that represents physical recombination between chromosomes.
ChIP-Chip:
Chromatin immunoprecipitation followed by hybridization of the precipitated DNA to a genomic microarray (chip).
ChIP-Seq:
Chromatin immunoprecipitation followed by DNA sequencing.
chiral:
Describes a compound that contains an asymmetric center (chiral atom or chiral center) and thus can occur in two nonsuperimposable, mirror-image forms (enantiomers).
chiral center:
An atom with substituents arranged so that the molecule is not superimposable on its mirror image.
chloramphenicol:
An antibiotic that inhibits protein synthesis by bacterial, mitochondrial, and chloroplast ribosomes by blocking peptidyl transfer.
chromatin:
A filamentous complex of DNA, histones, and other proteins, constituting the eukaryotic chromosome.
chromatin remodeling complex:
A protein complex with ATPase activity that translocates nucleosomes along the DNA, making certain regions of DNA more or less accessible to transcription factors.
chromatography:
A process in which complex mixtures of molecules are separated by many repeated partitionings between a flowing (mobile) phase and a stationary phase. The stationary phase may be packed into a tube (column chromatography) or planar (thin-layer chromatography).
chromodomain:
A protein structural motif that recognizes and binds certain methylated Lys residues in proteins.
chromosomal scaffold:
Proteinaceous residue after extraction of histones from chromosomes, consisting mainly of SMC proteins.
chromosome:
A single large DNA molecule and its associated proteins, containing many genes; stores and transmits genetic information.
chromosome theory of inheritance:
The hypothesis proposed by Walter Sutton in 1903 that genes are located on chromosomes.
clamp loader:
The portion of the E. coli DNA polymerase III holoenzyme that assembles the β sliding clamps onto the DNA.
clone:
An identical copy.
cloning:
The production of large numbers of identical DNA molecules, cells, or organisms from a single ancestral DNA molecule, cell, or organism.
cloning vector:
A DNA molecule known to replicate autonomously in a host cell, to which a segment of DNA may be spliced to allow its replication; for example, a plasmid or an artificial chromosome.
closed-circular DNA:
A continuous double-stranded DNA molecule with no free 3′ or 5′ ends.
closed complex:
A complex of the RNA polymerase bound to a promoter, in which the DNA is intact and double-stranded. Compare open complex.
closed form:
The conformation assumed by E. coli DNA polymerase I when a primed template and the correct dNTP are both bound to the active site.
CMG complex:
A complex of the proteins Cdc24, MCM helicase, and GINS proposed to function in the eukaryotic replisome.
coactivator:
A protein that stimulates transcription by binding both the RNA polymerase and an activator or activators, without binding the DNA directly. Compare corepressor and DNA-binding transcription activator.
coalescent theory:
Retrospective analysis of population genetics data (mutation rates, selection, genetic drift, and other factors) to trace a polymorphism back to the original ancestor in which it appeared.
coding strand:
The strand of a double-stranded DNA that has the same sequence as the RNA transcript (with T in place of U) and is complementary to the template strand. Also called the nontemplate strand.
codominance:
Non-Mendelian behavior in which two alleles of a gene produce distinct functional products, neither of which is dominant to the other. Compare incomplete dominance.
codon:
In a nucleic acid, a sequence of three adjacent nucleotides that codes for a specific amino acid.
codon bias:
The use of certain degenerate codons more than others to code for a given amino acid.
codon family:
A set of multiple codons that specify the same amino acid.
coenzyme:
An organic cofactor required for the action of certain enzymes; usually derived from a vitamin.
cofactor:
An inorganic ion or a coenzyme required for enzyme activity.
cohesins:
SMC proteins that link sister chromatids immediately after chromosomal replication and keep them together as the chromosomes condense to metaphase.
coiled-coil motif:
Protein motif in which two α helices twist around each other in a left-handed supercoil, interacting through hydrophobic contacts.
cointegrate:
An intermediate in the migration of certain DNA transposons in which the donor DNA and target DNA are covalently attached.
column chromatography:
A process in which complex mixtures of molecules are separated by many repeated partitionings between a flowing (mobile) phase and a stationary phase packed into a column.
combinatorial control:
The use of specific combinations of a limited number of regulatory proteins to exert fine control over gene expression.
comparative genomics:
The study of genome structure, function, and evolution by comparison across different species.
competitive inhibitor:
A molecule that competes with the normal substrate or ligand for a protein’s binding site.
complementary:
Having a molecular surface with chemical groups arranged to interact specifically with chemical groups on another molecule. Because of complementarity, if the nucleotide sequence of one strand of a double-stranded nucleic acid is known, the sequence of the opposite strand can be deduced.
complementary DNA (cDNA):
A duplex DNA with one strand identical to a specific mRNA (with T residues generally substituting for the U residues in the mRNA), used in DNA cloning; usually made by reverse transcriptase.
complex transposon:
A viruslike transposon with a large genome including genes not required for transposition.
composite transposon:
A transposon that consists of two insertion elements flanking one or more genes not required for transposition, such as antibiotic-resistance genes.
condensins:
SMC proteins that facilitate chromosomal condensation.
configuration:
An arrangement of bonded atoms that can be changed to a different configuration only by breaking and re-forming one or more covalent bonds.
conformation:
An arrangement of bonded atoms that can be changed to a different conformation without breaking and re-forming a covalent bond, such as by rotation about one or more single bonds.
consensus sequence:
A DNA or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences.
constitutive gene expression:
The continual expression of a gene. Compare regulated gene expression.
constructive interference:
Phenomenon in which waves in the same phase add to create waves of larger amplitude.
contig:
A series of overlapping clones or a continuous sequence defining an uninterrupted section of a chromosome.
cooperativity:
The characteristic of an enzyme or other protein in which binding of the first molecule of a ligand changes the affinity for the second molecule. In positive cooperativity, the affinity for the second ligand molecule increases; in negative cooperativity, it decreases.
core histones:
The four histone proteins (H2A, H2B, H3, and H4) that form the octameric core of the most common type of nucleosome.
corepressor:
A protein that inhibits transcription by binding both the RNA polymerase and a repressor or repressors, without binding the DNA directly. Compare coactivator.
core promoter:
In eukaryotic cells, the DNA sequence elements common to promoters used by Pol II. The TATA box and initiator sequence (Inr) are required elements of a core promoter; a TFIIB recognition element (BRE) and downstream promoter element (DPE) may also be involved in transcription initiation from some core promoters.
correlation spectroscopy (COSY):
A type of two-dimensional nuclear magnetic resonance spectroscopy in which atoms that are near to one another and connected through covalent bonds can be identified.
COSY:
See correlation spectroscopy.
covalent bond:
A chemical bond that involves sharing of electron pairs.
covalent modification:
The addition, dissociation, or rearrangement of an atom or functional group covalently bonded in a molecule. In biological systems, common modifying groups include acetyl, adenylyl, amide, carboxyl, hydroxyl, methyl, myristoyl, palmitoyl, phosphoryl, prenyl, sulfate, and uridylyl groups.
CpG sequence:
A DNA sequence (cytosine, guanine) that is a frequent substrate for cytosine methylation.
Cre-lox:
A bacteriophage-encoded site-specific recombination system that promotes circularization of the phage P1 genome and aids in proper segregation at cell division of phage plasmids in the lysogenic state.
crossing over:
The reciprocal exchange of DNA between paired homologous chromosomes during meiosis. Also called recombination.
cross-linking:
The use of a small chemical agent with two reactive groups to covalently link molecules that are in close proximity.
crossover:
See genetic crossover.
CRP:
See cAMP receptor protein.
cruciform:
A secondary structure in double-stranded RNA or DNA in which the double helix is denatured at palindromic repeat sequences in each strand, and each separated strand is paired internally to form opposing hairpin structures. See also hairpin.
C-terminus (carboxyl terminus):
See carboxyl terminus.
cyclic AMP (cAMP):
A second messenger, adenosine 3′,5′-cyclic monophosphate; its formation in a cell by adenylyl cyclase is stimulated by certain hormones or other molecular signals.
cyclic GMP (cGMP):
A second messenger, guanosine 3′,5′-cyclic monophosphate; its formation in a cell by guanylyl cyclase is stimulated by certain hormones or other molecular signals.
cyclobutane ring:
A structure formed by the condensation of two double-bonded C5=C6 atoms on adjacent pyrimidine bases in DNA.
cycloheximide:
An antibiotic that inhibits protein synthesis by eukaryotic ribosomes by blocking peptidyl transfer.
cytogenetics:
The study of chromosomes and their role in heredity.
cytokinesis:
The final separation of daughter cells following mitosis.
cytology:
The study of cells and cellular structures.
cytoplasmic membrane:
The exterior membrane surrounding the cytoplasm of a cell. Also called the plasma membrane.
cytosine (C):
A pyrimidine base that is a component of DNA and RNA.
cytotoxic:
Deadly to cells.
Dam methylase (DNA adenine methyltransferase):
An enzyme of E. coli that methylates adenine residues in the palindromic sequence GATC on both strands of the DNA. Transient hemimethylation of a DNA duplex following replication distinguishes the parental strand from the daughter strand.
DCC:
See dosage compensation complex.
DDE motif:
A protein secondary structure in which the amino acid residues D, D, and E (two aspartate residues and a glutamine residue) form the catalytic core in the active site of phosphoryltransferase enzymes such as integrases and transposases.
deamination:
The enzymatic removal of amino groups from biomolecules such as amino acids or nucleotides.
deep sequencing:
Extensive genomic sequencing designed to produce multiple (sometimes hundredfold or greater) coverage of all targeted sequences; used to detect sequence variants within a population.
degenerate code:
A code in which a single element in one language is specified by more than one element in a second language. The genetic code is degenerate because some amino acids are specified by more than one codon.
deletion analysis:
A method for assessing the functional importance of various regions of a protein by engineering a series of constructs with different parts of the gene deleted. The proteins expressed by these constructs can then be assayed for functionality.
deletion mutation:
A mutation resulting from the deletion of one or more nucleotides from a gene or chromosome. Compare insertion mutation.
denaturation:
The partial or complete unfolding of the specific native conformation of a polypeptide chain, protein, or nucleic acid such that the function of the molecule is lost. In the case of nucleic acids, also called melting.
deoxyribonucleic acid:
See DNA.
deoxyribonucleotide:
A nucleotide containing 2-deoxy-D-ribose as the pentose component. Also called a deoxynucleotide.
depurination:
The enzymatic removal of a purine base from a nucleotide.
Dicer:
An endonuclease in eukaryotic cells that catalyzes the hydrolysis of double-stranded RNAs, producing siRNAs or processing pre-miRNAs to mature miRNAs. Dicer also plays a role in the creation of RNA-induced silencing complexes.
diffraction pattern:
The interference pattern that results when a wave or series of waves is diffracted by an object with a regular structure, such as a crystal.
dimer:
A molecule with two subunits.
diphtheria toxin:
A bacterial toxin that catalyzes the ADP-ribosylation of a diphthamide (a modified histidine) residue of elongation factor eEF2, thereby inactivating it and inhibiting protein synthesis by the eukaryotic ribosome.
diploid:
Having two sets of genetic information; describes a cell with two chromosomes of each type. Compare haploid.
directionality:
The direction in which a process or enzyme proceeds along an asymmetric molecule. For example, certain endonucleases act on DNA only in a 5′ to 3′ direction.
dissociation constant (Kd):
An equilibrium constant for the dissociation of a complex of two biomolecules into its components; for example, dissociation of a substrate from an enzyme. Kd is the reciprocal of the association constant, Ka. Compare association constant (Ka)
distributive synthesis:
The enzymatic synthesis of a biological polymer in which the enzyme dissociates from the substrate after the addition of each monomeric unit. Compare processive synthesis.
disulfide bond:
A covalent bond involving the oxidative linkage of the sulfhydryl groups of two Cys residues, in the same or different polypeptide chains.
Dmc1:
A eukaryotic recombinase structurally and functionally homologous to the RecA protein of E. coli. See also Rad51.
DNA (deoxyribonucleic acid):
A polynucleotide with a specific sequence of deoxyribonucleotide units covalently joined through 3′,5′-phosphodiester bonds; serves as the carrier of genetic information.
DNA adenine methyltransferase:
See Dam methylase.
DNA-binding transactivator:
See DNA-binding transcription activator.
DNA-binding transcription activator:
In eukaryotic cells, a protein that binds to enhancers or UASs to facilitate transcription. Also called a DNA-binding transactivator. Compare coactivator.
DNA cloning:
See cloning.
DNA genotyping:
The process of defining particular genomic sequences associated with an individual. Also called DNA fingerprinting or DNA profiling.
DNA glycosylase:
An enzyme that hydrolyzes the N-β-glycosyl bond between a nucleotide base and pentose, creating an abasic site in the DNA.
DNA helicase:
See helicase.
DNA library:
A collection of cloned DNA fragments.
DNA ligase:
An enzyme that creates a phosphodiester bond between the 3′ end of one DNA segment and the 5′ end of another.
DNA looping:
The interaction of proteins bound at distant sites on a DNA molecule so that the intervening DNA forms a loop.
DNA microarray:
A collection of DNA sequences immobilized on a solid surface, with individual sequences laid out in patterned arrays that can be probed by hybridization. Also called a DNA chip.
DNA nuclease:
See nucleases.
DNA overwinding:
The condition in which a closed-circular DNA has more helical turns than would be expected of B-form DNA. Its linking number, Lk, is increased relative to that of B-form DNA, and the molecule is positively supercoiled.
DNA photolyase:
A flavoprotein enzyme that becomes an electron donor when activated by visible light. DNA photolyases can repair pyrimidine dimers and other lesions caused by ultraviolet light.
DNA polymerase:
An enzyme that catalyzes template-dependent synthesis of DNA from its deoxyribonucleoside 5′-triphosphate precursors.
DNA polymerase I:
A bacterial DNA polymerase engaged in DNA replication associated with DNA repair and processing of Okazaki fragments.
DNA polymerase II:
A bacterial DNA polymerase engaged in translesion DNA synthesis.
DNA polymerase III:
The primary replicative DNA polymerase in bacteria.
DNA polymerase IV:
A bacterial DNA polymerase engaged in translesion DNA synthesis.
DNA polymerase V:
A bacterial DNA polymerase engaged in translesion DNA synthesis.
DNA polymerase α (Pol α):
A eukaryotic DNA polymerase with both primase and error-prone DNA polymerase activities. The enzyme synthesizes an RNA primer on a DNA template and then extends it with DNA.
DNA polymerase δ (Pol δ):
A eukaryotic chromosomal replicase with both DNA polymerase and 3′→5′ exonuclease activities. It acts on the lagging strand of the replication fork.
DNA polymerase ε (Pol ε):
A eukaryotic chromosomal replicase with both DNA polymerase and 3′→5′ exonuclease activities. It acts on the leading strand of the replication fork.
DNA replication:
The synthesis of daughter DNA molecules identical to the parental DNA.
DNA strand invasion:
The pairing of a single-stranded extension of a DNA molecule with a homologous region of another DNA molecule, with displacement of one strand of the recipient molecule by the invading strand.
DNA supercoiling:
The coiling of DNA upon itself, generally as a result of bending, underwinding, or overwinding of the DNA helix.
DNA topology:
The properties of DNA that do not change under continuous deformations such as twisting, bending, stretching, or binding other molecules.
DNA underwinding:
The condition in which a closed-circular DNA has fewer helical turns than would be expected of B-form DNA. Its linking number, Lk, is reduced relative to that of B-form DNA, and the molecule is negatively supercoiled.
domain:
A distinct structural unit of a polypeptide; domains may have separate functions and may fold as independent, compact units.
dominant:
Describes the allele that determines the phenotype in a heterozygous individual. Compare recessive.
donor site:
The location on a chromosome of a transposon before it moves to a target site. Compare target site.
dosage compensation:
The control of gene expression from sex chromosomes to ensure that male and female cells express similar levels of each gene product.
dosage compensation complex (DCC):
A ribonucleoprotein complex encoded by the X chromosome in Drosophila. The complex coats the single X chromosome in male cells, hyperstimulating transcription from its genes to compensate for the lack of a second X chromosome.
double bond:
A bond between two elements that involves four electrons instead of two.
double-strand break (DSB):
A break in the phosphodiester backbone of both strands of a double-stranded nucleic acid.
double-strand break repair (DSBR):
A method for repairing double-strand breaks that creates two Holliday intermediates, which must be cleaved by resolvases. The genes flanking the repair site may be unchanged or may undergo a reciprocal exchange, depending on how the crossovers are resolved.
Drosha:
An endonuclease in eukaryotic cells that cleaves the hairpin of primary miRNA transcripts to produce pre-miRNAs.
DSB:
See double-strand break.
DSBR:
See double-strand break repair.
duplication mutation:
The duplication of a large tract of DNA, leading to an increased dosage of genes in the affected area.
editosome:
A protein complex that catalyzes the insertion or deletion of nucleotide residues during the process of RNA editing.
eEF1α:
In eukaryotic protein synthesis, an elongation factor that delivers aminoacyl-tRNAs to the A site of the elongation complex with the concomitant hydrolysis of bound GTP.
eEF1βγ:
In eukaryotic protein synthesis, an elongation factor that uses bound GTP to regenerate eEF1α-GTP from eEF1α-GDP.
eEF2:
In eukaryotic protein synthesis, an elongation factor with GTPase activity. GTP hydrolysis provides the energy for the ribosome to translocate along the mRNA to the next codon. Also called a translocase.
effector:
A small molecule that binds a transcription activator or repressor, causing a conformational change in the regulatory protein that results in an increase or decrease in transcription from the gene.
EF-G:
In bacterial protein synthesis, an elongation factor with GTPase activity. GTP hydrolysis provides the energy for the ribosome to translocate along the mRNA to the next codon. Also called a translocase.
EF-Ts:
In bacterial protein synthesis, an elongation factor that uses bound GTP to regenerate EF-Tu-GTP from EF-Tu-GDP.
EF-Tu:
In bacterial protein synthesis, an elongation factor that delivers aminoacyl-tRNAs to the A site of the elongation complex with the concomitant hydrolysis of bound GTP.
EJC:
See exon junction complex.
electric dipole moment:
A measure of the electrical polarity of a bond or molecule. It is equal to the magnitude of the charge times the distance separating the charges.
electron density map:
A three-dimensional description of the electron density in a crystal, derived from x-ray diffraction data.
electronegative atoms:
Atoms with a tendency to gain electrons.
electronegativity:
The propensity of an atom to attract electrons to itself.
electrophoresis:
See gel electrophoresis.
electroporation:
Introduction of macromolecules into cells after rendering the cells transiently permeable by the application of a high-voltage pulse.
electropositive atoms:
Atoms with a tendency to lose electrons.
elongation:
(1) The second of three stages of RNA synthesis, in which ribonucleotides are added to the 3′ end of the growing RNA molecule. (2) The second of three stages of protein synthesis, in which amino acids are added to the C-terminal end of the growing peptide chain.
elongation complex:
The complex of proteins required for efficient synthesis of the RNA transcript after the RNA polymerase has moved beyond the promoter.
elongation factors:
(1) Proteins required in the elongation phase of eukaryotic transcription. (2) Proteins required in the elongation phase of protein synthesis. See also eEF1α, eEF1βγ, eEF2, EF-G, EF-Ts, and EF-Tu.
embryonic stem cells:
The cells in a mammalian embryo that retain the ability to divide and differentiate into other cell types. Compare adult stem cells.
enantiomers:
Stereoisomers that are nonsuperimposable mirror images of each other.
endonuclease:
An enzyme that hydrolyzes the interior phosphodiester bonds of a nucleic acid; that is, it acts at bonds other than the terminal bonds.
end replication problem:
The inability of DNA polymerases to replicate the final segment of DNA at the 3′ end of the lagging strand where there is no primer to provide a free 3′-OH group.
enhanceosome:
A nucleoprotein complex of cooperating activators, which integrates regulatory information from multiple signals and generates a single transcriptional outcome at the target promoter.
enhancer:
A DNA sequence that facilitates the expression of a given gene; it may be located a few hundred, or even thousand, base pairs away from the gene. In yeast, enhancers are called upstream activator sequences (UASs).
entropy (S):
The extent of randomness or disorder in a system.
enzyme:
A biomolecule, either protein or RNA, that catalyzes a specific chemical reaction. It does not affect the equilibrium of the catalyzed reaction; it enhances the rate of the reaction by providing a reaction path with lower activation energy.
enzyme kinetics:
The study of the rates of reactions catalyzed by enzymes.
epigenetic inheritance:
The inheritance of characteristics acquired by means that do not involve the nucleotide sequence of the parental chromosomes; for example, covalent modifications of histones.
epitope tag:
A protein sequence or domain bound by some well-characterized antibody.
equilibrium expression:
A mathematical expression for the equilibrium constant of a chemical reaction, expressed as the product of the molar concentrations of each reaction product, raised to its coefficient in the balanced reaction, over the product of the molar concentrations of each reactant, raised to its coefficient in the balanced reaction.
E site:
The site in a ribosome occupied by the tRNA molecule released after the growing polypeptide chain is transferred to the aminoacyl-tRNA. Also called the exit site.
EST:
See expressed sequence tag.
euchromatin:
The regions of interphase chromosomes that stain diffusely, as opposed to the more condensed, heavily staining, heterochromatin. These are often regions in which genes are being actively expressed.
eukaryotes:
One of the three main groups of living organisms; eukaryotes are unicellular or multicellular organisms with cells having a membrane-bounded nucleus, multiple chromosomes, and internal organelles.
evo-devo:
The field of evolutionary development, which demonstrates that dramatic phenotypic differences between species can be accounted for by changes in the temporal expression of shared or homologous genes and regulatory networks.
evolution:
A process in which the population of a species changes over time. Genetic variation occurs in the populations due to mutation; competitive pressures in the environment lead to the natural selection of individuals whose genetic makeup gives them a reproductive advantage. Over time, the genetic makeup of the surviving population shifts, sometimes creating new species.
excinuclease:
An enzyme that cleaves a phosphodiester bond in the DNA on either side of a bulky lesion in DNA. Also called an excision endonuclease.
exon:
The segment of a eukaryotic gene that encodes a portion of the final product of the gene; a segment of RNA that remains after posttranscriptional processing and is transcribed into a protein or incorporated into the structure of an RNA. Compare intron.
exon junction complex (EJC):
A complex of proteins deposited on an mRNA by the spliceosome 20 to 24 nucleotides upstream of exon-exon junctions.
exonuclease:
An enzyme that hydrolyzes only those phosphodiester bonds that are in the terminal positions of a nucleic acid.
exosome:
A complex of 3′→5′ exonucleases in eukaryotic cells that processes the 3′ ends of rRNAs and tRNAs and is responsible for RNA degradation in higher eukaryotes.
exothermic reaction:
A chemical reaction that releases heat (that is, for which ΔH is negative).
exportin:
A protein receptor responsible for transporting RNAs from the nucleus, through a nuclear pore, into the cytoplasm.
expressed sequence tag (EST):
A specific type of sequence-tagged site in DNA representing a gene that is expressed.
expression vector:
A cloning vector with the transcription and translation signals needed for the regulated expression of a cloned gene. See also cloning vector.
extrachromosomally primed (EP) retrotransposon:
A retrotransposon that moves via a double-stranded cDNA copy of its mRNA transcript. The cDNA inserts itself into the target site in a reaction catalyzed by a recombinase or integrase. See also target-primed (TP) retrotransposon.
first law of thermodynamics:
The law stating that, in all processes, the total energy of the universe remains constant.
5′ cap:
A residue of 7-methylguanosine (7-meG) linked to the 5′-terminal residue of an mRNA through a 5′,5′-triphosphate linkage, which protects the mRNA from exoribonucleases.
F1 generation:
The first filial generation, the hybrid offspring in a genetic cross.
fork regression:
Backward movement of the replication fork, which can occur when a replication fork encounters a lesion and stalls. Fork regression allows the parental strands to reanneal until the lesion is repaired.
four-helix bundle:
A supersecondary protein structure in which four α helices associate through hydrophobic interactions.
frameshift mutation:
A mutation caused by insertion or deletion of one or more paired nucleotides, changing the reading frame of codons during protein synthesis; the polypeptide product has an altered amino acid sequence beginning at the mutated codon.
free energy (G):
The component of the total energy of a system that can do work at constant temperature and pressure.
free-energy change (ΔG):
The amount of free energy released (negative ΔG) or absorbed (positive ΔG) in a reaction at constant temperature and pressure.
F2 generation:
The second filial generation, the offspring of crossing the F1 generation.
functional RNA:
An RNA molecule that is a functional end product, as distinct from messenger RNA (mRNA), which serves as a transient intermediary between DNA and a protein product it encodes.
fusion gene:
A hybrid gene formed when chromosomal DNA is rearranged by deletion, duplication, insertion, or transposition.
fusion protein:
The protein product of a gene created by the fusion of two distinct genes or portions of genes.
gamete cell:
A reproductive cell with a haploid gene content; a sperm or egg cell.
gap genes:
A subclass of the segmentation genes involved in dividing the developing Drosophila embryo into broad regions. Gap genes are expressed before the pair-rule genes.
gap repair:
A process for repairing gaps left when the replication fork bypasses a lesion.
gel electrophoresis:
A technique for separating mixtures of large charged molecules such as proteins or nucleic acids by causing them to move through a gel matrix in an applied electric field.
gel-exclusion chromatography:
A type of column chromatography in which molecules are separated by size, based on the capacity of porous polymers to exclude solutes above a certain size.
gene:
A chromosomal segment that codes for a single functional polypeptide chain or RNA molecule.
gene conversion:
A nonreciprocal transfer of genetic information as an outcome of DNA repair, especially during meiosis.
general rate constant (kcat):
The constant defined by the limiting rate of an enzyme-catalyzed reaction. It describes the number of substrate molecules converted to product by a single molecule of enzyme at saturating levels of substrate. The constant has units of reciprocal time. See also turnover number.
general transcription factor:
In eukaryotic cells, a protein required at every Pol II promoter. Also called a basal transcription factor.
gene silencing:
(1) The suppression of gene expression by incorporation of the gene into transcriptionally inactive heterochromatin. (2) The suppression of gene expression by short interfering RNAs, which bind mRNAs and target them for degradation.
genetic code:
The set of triplet code words in DNA (or mRNA) coding for the amino acids of proteins.
genetic crossover:
Any redistribution of genes between two homologous chromosomes that results from a chromosomal crossover.
genetic drift:
The change in frequency of an allele in a population due to random sampling, rather than selective pressure. Genetic drift is affected by such variables as the number of reproducing individuals in a population and the number of offspring generated.
genetic engineering:
Manipulation of an organism’s genome in the laboratory.
genetics:
The science of heredity and the variation of inherited characteristics.
genome:
One copy of all the genetic information encoded in a cell or virus. In a eukaryote, this generally constitutes one copy of all the genetic information in the nucleus. Separate genomes are found in certain organelles, particularly mitochondria and chloroplasts.
genome annotation:
Information about the location and function of genes and other regulatory and functional sequences in a genome.
genome editing:
The precise introduction, alteration, or removal of sequences in a genome using a variety of sequence-targeted methods.
genomic library:
A DNA library containing DNA segments that represent all (or most) of the sequences in an organism’s genome.
genomics:
Broadly, the study of genomes. Genomics embraces sequencing, mapping, and annotating genomes; organizing databases to archive genomic data; developing computational tools to analyze the data; and application of genomic data to other fields, such as medicine.
genotoxic:
Causing damage to the genomic DNA.
genotype:
The genetic constitution of an organism, as distinct from its physical characteristics, or phenotype.
genotyping:
See DNA genotyping.
GFP:
See green fluorescent protein.
glycosidic bonds:
Bonds formed between a sugar and another molecule (typically an alcohol, purine, pyrimidine, or sugar) through an intervening oxygen.
G1 phase:
The first gap phase of the eukaryotic cell cycle, in which the cell is diploid. G1, part of interphase, occurs before the S (synthesis) phase, in which the DNA is replicated.
GPCR:
See G protein–coupled receptor.
G protein–coupled receptor (GPCR):
Any of a large family of membrane receptor proteins with seven transmembrane helical segments, often associating with G proteins to transduce an extracellular signal into a change in cellular metabolism.
Greek key motif:
Supersecondary protein motif in which four antiparallel β strands combine in a pattern seen on ancient Greek pottery.
green fluorescent protein (GFP):
A small protein that produces a bright fluorescence in the green region of the visible spectrum. Fusion proteins with GFP are commonly used to determine the subcellular location of the fused protein by fluorescence microscopy. Variants that produce other colors, such as red fluorescent protein (RFP) and cyan fluorescent protein (CFP), have also been produced.
group I intron:
A large, self-splicing ribozyme that catalyzes its own excision from an mRNA, tRNA, or rRNA transcript in a reaction that requires a guanosine nucleotide or nucleoside to initiate the reaction.
group II intron:
A large, self-splicing ribozyme that catalyzes its own excision from an mRNA transcript as a lariat structure.
G tetraplex:
A four-stranded DNA structure that can form from G-rich segments of DNA.
G2 phase:
The second gap phase of the eukaryotic cell cycle, in which the cell is tetraploid. G2, part of interphase, occurs between the S (synthesis) phase and the M (mitosis) phase.
guanine (G):
A pyrimidine base that is a component of DNA and RNA.
guanosine 3′,5′-cyclic monophosphate:
See cyclic GMP.
hairpin:
A secondary structure in single-stranded RNA or DNA, in which complementary parts of a palindromic repeat fold back and are paired to form an antiparallel duplex helix that is closed at one end.
haploid:
Having a single set of genetic information; describes a cell with one chromosome of each type. Compare diploid.
haplotype:
(1) In genetics, a group of alleles on a chromosome that are nearly always inherited together. (2) In genomics, a set of single-nucleotide polymorphisms that are nearly always inherited together.
HAT:
See histone acetyltransferase.
helicase:
An enzyme that catalyzes the separation of strands in a nucleic acid molecule in a reaction coupled to the hydrolysis of ATP.
helix-turn-helix motif:
A supersecondary protein motif consisting of two α helices separated by a β turn. This motif is crucial to the interaction of many bacterial regulatory proteins with DNA.
heterochromatin:
The condensed, heavily staining portions of chromosomes that are not transcriptionally active, including centromeres, telomeres, some repetitive DNA sequences, and mitotic chromosomes.
heterocyclic compound:
A molecule incorporating one or more rings that incorporate atoms of different elements.
heterooliogmer:
A multisubunit molecule (oligomer) with nonidentical subunits.
heterotropic:
Describes an allosteric modulator that is distinct from the normal ligand or an allosteric enzyme requiring a modulator other than its substrate.
heterozygous:
Having different alleles at a specific genetic locus.
hierarchical model:
A model for protein folding that proposes that local regions of secondary structure form first, followed by longer-range interactions, continuing until complete domains form and the entire polypeptide is folded. Compare molten globule model.
high-mobility group (HMG) proteins:
Three families of chromosomal proteins that bind DNA nonspecifically, promoting chromatin remodeling and DNA looping for regulating DNA transcription.
histone acetyltransferase (HAT):
Any of a family of enzymes that transfer an acetyl group from acetyl-CoA to the ε-amino group of specific Lys residues on histone tails.
histone chaperones:
Acidic proteins required for the assembly of histone octamers on DNA.
histone code:
A hypothetical code in which successive covalent modifications of histone tails and DNA trigger chromatin remodeling and transcriptional activation events.
histone-fold motif:
A protein structural motif formed from three α helices connected by two loops. Histone-fold dimers are instrumental in the tight wrapping of the DNA helix around the histone core in nucleosomes.
histone modifying enzymes:
A class of enzymes that covalently modify the N-terminal tails of histones.
histone octamer:
The complex of two copies of each of the four core histones that forms the histone core of the nucleosome.
histones:
The family of basic proteins that associate tightly with DNA in the chromosomes of all eukaryotic cells.
histone tails:
The flexible, disordered N-terminal ends of the histone proteins that comprise the histone core. These ends protrude from the nucleosome and contact adjacent nucleosomes.
HMG proteins:
See high-mobility group (HMG) proteins.
Holliday intermediate:
An intermediate in genetic recombination in which two double-stranded DNA molecules are joined by a reciprocal crossover involving one strand of each molecule to form a junction with four DNA branches.
Holliday junction resolvase:
A nuclease that specifically binds to and cleaves Holliday intermediates.
holoenzyme:
A catalytically active enzyme, including all necessary subunits, prosthetic groups, and cofactors.
homeodomain motif:
A conserved 60 amino acid sequence motif in transcription activators encoded by genes that regulate body pattern development.
homeotic genes:
Genes that regulate development of the pattern of segments in the Drosophila body plan; similar genes are found in most vertebrates. Homeotic genes are expressed after the segmentation genes.
homing endonucleases:
Intron-encoded restriction endonucleases that recognize and cleave an asymmetric sequence of 12 to 40 base pairs in the cellular DNA. Repair of the break results in insertion of a copy of the intron via homologous recombination.
homologous chromosomes:
In diploid organisms, a pair of chromosomes, one inherited from each parent, that are of similar length, structure, and gene sequence. Also called homologs.
homologous recombination:
Recombination between two DNA molecules of similar sequence, occurring in all cells; takes place during meiosis and mitosis in eukaryotes and during the repair of double-strand breaks in all organisms.
homologs:
Genes or proteins with sequence similarity. Also shorthand for homologous chromosomes.
homooligomer:
Multisubunit molecule (oligomer) with identical subunits.
homotropic:
Describes an allosteric modulator that is identical to the normal ligand or an allosteric enzyme that uses its substrate as a modulator.
homozygous:
Having identical alleles at a specific genetic locus.
Hoogsteen pairing:
Non-Watson-Crick pairing of a pyrimidine base to a purine base that is already participating in a Watson-Crick base pair with another pyrimidine. The arrangement allows the formation of triplex DNA.
Hoogsteen position:
The atoms in a purine base that participate in Hoogsteen pairs (non-Watson-Crick hydrogen bonding) with a pyrimidine base.
horizontal gene transfer:
The process by which an organism receives genetic information from another organism of which it is not a descendant.
hormone response element (HRE):
A short (12 to 20 bp) DNA sequence that binds receptors for steroid, retinoid, thyroid, and vitamin D hormones, altering the expression of the contiguous genes. Each hormone has a consensus sequence preferred by the cognate receptor.
housekeeping gene:
A gene that must be expressed continually for the cell to survive.
Hox genes:
A major class of homeotic genes.
HRE:
See hormone response element.
Hsp70:
A family of heat-shock proteins with Mr ≈ 70,000 that constitute a class of molecular chaperones.
hybrid:
The offspring of a cross between genetically nonidentical individuals.
hybrid duplex:
A duplex experimentally reconstituted from single-stranded DNA (or RNA) from different sources.
hydrogen bond:
A weak electrostatic attraction between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom.
hydrolysis:
Cleavage of a bond, such as an anhydride or peptide bond, by the addition of the elements of water, yielding two or more products.
hydrophobic effect:
The association of nonpolar groups or compounds with each other in aqueous systems, driven by the tendency of the surrounding water molecules to seek their most stable (disordered) state.
hydrophobic interactions:
See hydrophobic effect.
hydrophobic stacking:
See base stacking.
hyperchromic effect:
The large increase in light absorption at 260 nm occurring as a double-helical DNA unwinds (melts). Compare hypochromic effect.
hypersensitive site:
A DNA sequence within a chromosome that is especially sensitive to cleavage by DNase I and other nucleases due to the relative absence of binding proteins such as histones. These sites typically precede active promoters and may be binding sites for proteins regulating expression from the downstream gene.
hypochromic effect:
The large decrease in light absorption at 260 nm occurring as single strands of DNA anneal to form double-helical DNA. Compare hyperchromic effect.
hypothesis:
A proposal that provides a reasonable explanation for observations, but has not yet been substantiated by sufficient experimental evidence to stand up to rigorous critical examination.
IF-1:
In bacterial protein synthesis, an initiation factor that binds the ribosomal A site and blocks tRNA binding.
IF-3:
In bacterial protein synthesis, an initiation factor that prevents premature addition of the 50S ribosomal subunit to the assembling initiation complex.
IF-2:
In bacterial protein synthesis, an initiation factor that directs the initiating tRNA to the P site of the 30S subunit. When the 50S subunit binds to the complex, it hydrolyzes the GTP bound to IF-2, releasing IF-2 and allowing the 70S subunit to form.
immunofluorescence:
The labeling of antibodies with a fluorescent dye to visualize or quantify an antigen in a biological, biochemical, or histological preparation.
immunoprecipitation:
The use of antibodies against an epitope on a protein of interest (often with secondary antibodies against those primary antibodies) to precipitate the protein from a complex mixture.
importin:
A protein receptor responsible for transporting noncoding RNAs processed in the cytoplasm into the nucleus through a nuclear pore.
imprinting:
An epigenetic method of regulating gene expression based on the parental origin of the gene.
incomplete dominance:
A condition in which alleles at a specific locus are neither dominant nor recessive, and the progeny express a phenotype intermediate between those of the two parents. Compare codominance.
indel:
A collective term for insertion and deletion mutations.
induced fit:
A change in the conformation of an enzyme in response to substrate binding that renders the enzyme catalytically active; also used to denote changes in the conformation of any macromolecule in response to ligand binding such that the binding site of the macromolecule better conforms to the shape of the ligand.
inducer:
A signal molecule that, when bound to a regulatory protein, produces an increase in the expression of a given gene.
initial model:
A protein structure derived from an electron density map before further refinements are made.
initial velocity (V0):
The velocity of a reaction while the concentration of substrate is saturating and can be regarded as constant relative to the enzyme concentration.
initiation:
(1) The first of three stages in the synthesis of DNA, in which the DNA polymerase binds to the origin of replication. (2) The first of three stages in the synthesis of RNA, in which the RNA polymerase binds to the promoter sequence on the DNA. (3) The first of three stages in the synthesis of a protein, in which the ribosome binds to the mRNA and initiator aminoacyl-tRNA.
initiation codon:
AUG (sometimes GUG or, even more rarely, UUG in bacteria and archaea); codes for the first amino acid in a polypeptide sequence: N-formylmethionine in bacteria; methionine in archaea and eukaryotes. Also called a start codon.
initiation complex:
A complex of a ribosome with an mRNA and the initiating Met-tRNAiMet or fMet-tRNAfMet, ready for the elongation steps.
initiation factors:
Three protein factors required to assemble the ribosomal subunits and initiator tRNA in preparation for protein synthesis in bacteria. See also IF-1, IF-2, and IF-3.
initiator protein:
A protein that binds specific sites in an origin of replication and serves as a nucleation site for the assembly of other protein complexes necessary to initiate replication; for example, DnaA in E. coli, and ORC in eukaryotes.
insertion mutation:
A mutation caused by insertion of one or more extra bases between successive bases in DNA. Compare deletion mutation.
insertion sequence:
A specific base sequence at either end of a transposable segment of DNA.
insertion site:
A site within the active site of a DNA polymerase where the template nucleotide and incoming dNTP are positioned. Compare postinsertion site.
insulator:
A short sequence of DNA that prevents inappropriate cross-signaling between regulatory elements for different genes. Also called a boundary element.
integrase:
An enzyme that catalyzes the insertion of a retrovirus or retrotransposon into its target site.
internal ribosome entry site (IRES):
A site on the 5′ side of the start codon in some viral and eukaryotic mRNAs where a eukaryotic ribosome can bind in the absence of a 5′ cap.
interphase:
The portion of the cell cycle that does not include mitosis. Subdivided into three phases: G1 phase, S phase, and G2 phase.
intervening sequence:
See intron.
intrinsically unstructured protein or protein segment:
A protein or segment of a protein that does not fold into an identifiable stable structure in solution. Intrinsically unstructured protein segments often take up a particular structure when they interact with another macromolecule.
intron:
A sequence of nucleotides in a gene that is transcribed but excised before the gene is translated. Also called an intervening sequence. Compare exon.
inversion mutation:
A mutation that results from the inversion of a large segment of DNA in a chromosome.
inverted repeat:
A sequence that is the reversed complement of a downstream sequence.
ion-exchange chromatography:
A type of column chromatography in which molecules are separated by charge, using a stationary phase that contains fixed charged groups.
ionic bond:
A chemical bond in which the electrons of one atom are transferred to another, creating positive and negative ions that attract each other.
ion torrent:
A method for rapid DNA sequencing.
IRE:
See iron response element.
IRES:
See internal ribosome entry site.
iron homeostasis:
The maintenance of a dynamic steady-state concentration of cellular iron by regulatory mechanisms that compensate for changes in external circumstances.
iron response element (IRE):
A hairpin structure in the 3′ or 5′ untranslated region of the mRNAs for proteins involved in iron homeostasis. Binding of the iron response protein (IRP) to a 5′ IRE inhibits translation of the mRNA; binding of IRP to a 3′ IRE inhibits degradation of the mRNA.
iron response protein (IRP):
A protein that binds the iron response element (IRE) in mRNAs for proteins involved in iron homeostasis, inhibiting their translation or degradation in response to the cell’s need for iron. Iron-sulfur centers required for efficient binding of IRPs to IREs form only when iron is plentiful in the cell and therefore serve as a sensor of the cellular level of iron.
IRP:
See iron response protein.
irreversible inhibitor:
A molecule that either forms a stable noncovalent association with an enzyme or binds the enzyme covalently, destroying a functional group necessary for its catalytic activity.
isoenergetic:
Describes a chemical reaction in which the reactants and products have the same or very similar free energy and therefore exist at similar concentrations at equilibrium.
Ka:
See association constant.
karyopherins:
A family of nuclear transport receptors including importins and exportins.
Kd:
See dissociation constant.
kinetic proofreading:
A mechanism for error correction in complex biological processes that maximizes the speed of correct reactions while stalling and allowing incorrect reactions to reverse.
kinetics:
The study of reaction rates.
Km:
See Michaelis-Menten constant.
Kozak sequence:
A sequence around the start codon in eukaryotic mRNA that enhances its translation. The Kozak sequence has a purine nucleotide three residues before, and a G residue immediately after, the start codon.
lagging strand:
The DNA strand that, during replication, must be synthesized in the direction opposite to that in which the replication fork moves.
last universal common ancestor:
See LUCA.
law of independent assortment:
In the formation of gametes there is an independent assortment of alleles for different genes. Also known as Mendel’s second law.
law of segregation:
In the formation of gametes there is an equal segregation of alleles. In other words, a haploid gamete contains one copy of each gene. Also known as Mendel’s first law.
leader peptide:
A short sequence near the amino terminus of a protein that has a specialized targeting or regulatory function.
leader sequence:
A short sequence near the 5′ end of an RNA that has a specialized targeting or regulatory function.
leading strand:
The DNA strand that, during replication, is synthesized in the same direction in which the replication fork moves.
leucine zipper motif:
A protein structural motif involved in protein-protein interactions in many eukaryotic regulatory proteins; consists of two interacting α helices in which Leu residues in every seventh position are a prominent feature of the interacting surfaces.
ligand:
Any molecule, small or large, that is specifically bound by a protein without altering that bound molecule; for example, a hormone is the ligand for its specific protein receptor.
linkage analysis:
The use of bioinformatics to analyze the statistical association between inheritance of a gene and the presence of specific single-nucleotide polymorphisms, with the goal of mapping the gene to a specific location on a chromosome.
linked genes:
Genes that are close together on a chromosome and the alleles of which therefore assort together during meiosis, in contradiction to Mendel’s second law.
linker:
A synthetic DNA fragment inserted into a cloning vector, usually to provide a specific desired sequence, such as a restriction endonuclease recognition sequence.
linker histone:
The histone protein H1, which binds to the linker DNA adjacent to the nucleosome.
linking number (Lk):
The number of times one closed circular DNA strand is wound about another; the number of topological links holding the circles together.
LUCA (last universal common ancestor):
The single-celled organism that gave rise to all life currently existing on Earth.
lysis:
Destruction of a plasma membrane or (in bacteria) cell wall, releasing the cellular contents and killing the cell.
lysogen:
A bacterial cell infected with a prophage.
lysogenic pathway:
Bacteriophage infection in which the DNA is incorporated into the host chromosome or as an autonomously replicating plasmid with most of its genes repressed. Compare lytic pathway.
lytic pathway:
Parasitic bacteriophage infection in which the DNA is replicated and packaged into phage heads, and the host cell is destroyed by lysis to disperse the progeny. Compare lysogenic pathway.
major groove:
The wider of two grooves that wind around the outside of a DNA double helix.
mass spectrometry (MS):
An analytical technique for determining the mass of a molecule, thus providing a clue to its identity, by measuring the charge-to-mass ratio of gaseous ions formed from the molecule as the ions pass through an electromagnetic field in a vacuum.
maternal genes:
Genes expressed in the unfertilized egg that are required for development of the early embryo.
maternal mRNAs:
Transcripts of maternal genes that are generated in the egg during oogenesis and remain dormant until fertilization.
mating type:
In yeast, one of the two haploid forms, a and α, that can mate only with a haploid cell of the opposite type to form a diploid cell.
maximum velocity:
See Vmax.
MCM complex:
A ring-shaped eukaryotic helicase complex that acts at the replication fork. It is composed of six homologous, but nonidentical, AAA+ proteins and interacts with two other proteins to form the CMG complex.
Mediator complex:
A large, multiprotein complex in eukaryotic cells that serves as the mediator between the Pol II transcription complex and any upstream transcription activators or enhancers regulating Pol II–catalyzed transcription.
meiosis:
A type of cell division in which diploid cells give rise to haploid cells destined to become gametes.
melting:
The denaturation or unwinding of a double-stranded polynucleotide to form single-stranded polynucleotides.
melting point (Tm):
The temperature at which a specific double-stranded polynucleotide separates into single strands.
messenger RNA (mRNA):
A class of RNA molecules, each of which is complementary to one strand of DNA, that carry the genetic message from the chromosome to the ribosomes.
metagenomics:
The structural and functional analysis of the collective genome of an environmental population of microorganisms rather than a pure population derived from a single cultured cell.
metamerism:
The division of the body into a series of repeating segments, such as in insects.
metaphase:
The second stage of mitosis (M phase). The spindle apparatus directs condensed sister chromatid pairs to align along the metaphase plate.
metaphase plate:
The equatorial plane in a dividing cell along which chromosomes align during metaphase.
Michaelis-Menten constant (Km):
The substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half its maximum velocity.
Michaelis-Menten equation:
The equation describing the hyperbolic dependence of the initial reaction velocity, V0, on substrate concentration, [S], in many enzyme-catalyzed reactions.
microprocessor complex:
A nuclear complex responsible for the early stages of miRNA and siRNA processing in eukaryotic cells. It consists of a primary miRNA transcript, an miRNA recognition protein, and the endonuclease Drosha.
microRNA (miRNA):
A class of small RNA molecules (21 to 23 nucleotides after processing is complete) involved in gene silencing by inhibiting translation and/or promoting the degradation of particular mRNAs.
migration:
(1) The movement of a population to a new geographic location. (2) The movement of cells to a new location within an organism or tissue.
minor groove:
The narrower of two grooves that wind around the outside of a DNA double helix.
mirror repeat:
A segment of duplex DNA in which the base sequences exhibit symmetry on each single strand.
mismatch repair (MMR):
An enzymatic system for repairing base mismatches (non-Watson-Crick pairs) in DNA.
missense mutation:
A single-nucleotide change in a gene that results in an amino acid change in the protein product.
mitosis:
In eukaryotic cells, the multistep process that results in the segregation of replicated cellular chromosomes and cell division.
mixed inhibitor:
An inhibitor molecule that can bind to either the free enzyme or the enzyme-substrate complex (not necessarily with the same affinity).
MMR:
See mismatch repair.
modulator:
See allosteric modulator.
MOI:
See multiplicity of infection.
mole:
One gram molecular weight of a compound. A mole of any compound contains 6.02 × 1023 molecules.
molecular biology:
The study of essential cellular macromolecules, including DNA, RNA, and proteins, and the biological pathways that link their biosynthesis.
molecular function (of a gene product):
The precise biochemical activity of a protein or an RNA, such as the reactions an enzyme catalyzes, the ligands a receptor binds, or the complex formed between a specific RNA and a protein. Compare cellular function and phenotypic function.
molecular genetics:
The study of the structure and function of genes at the molecular level.
molecular orbital model:
A mathematical function describing the wavelike behavior of electrons in a molecule.
molten globule model:
A model for protein folding in which the hydrophobic residues of a polypeptide chain rapidly collapse into a condensed, partially ordered state, which limits the conformations available to the rest of the molecule. As subdomains with tertiary structure develop, alternative conformations become increasingly limited, and the molecule achieves its native conformation. Compare hierarchical model.
motif:
See sequence motif; structural motif.
motor protein:
A protein that uses energy (typically from the hydrolysis of ATP) to undergo a cyclic conformational change that creates a unified, directional force.
M phase:
The phase of the eukaryotic cell cycle during which mitosis, or cell division, occurs. The M phase follows the G2 phase and precedes the G1 phase.
MS:
See mass spectrometry.
multiplicity of infection (MOI):
The ratio of infectious particles to target cells.
multipotent:
Describes stem cells that can differentiate into a number of types of closely related cells.
mutation:
An inheritable change in the nucleotide sequence of a chromosome.
mutation rate:
The frequency of new mutations (in a gene or in an organism) in each cellular generation.
natural selection:
The process by which traits (phenotypes) become more prevalent in a population because those individuals best adapted to exploit the prevailing resources are the ones most likely to survive and reproduce, passing on their advantageous traits.
negative regulation:
The decreased expression of a gene due to the binding of a repressor protein. Compare positive regulation.
negative supercoiling:
The twisting of a helical (coiled) molecule on itself to form a right-handed supercoil.
NER:
See nucleotide excision repair.
N-formylmethionyl-tRNAfmet:
The charged tRNA used to initiate protein synthesis in bacteria.
NHEJ:
See nonhomologous end joining.
niche:
In cellular differentiation, a microenvironment that allows the maintenance of both multipotent adult stem cells and their differentiated progeny.
nick translation:
A concerted process of 5′→3′ excision and DNA polymerization that shifts a discontinuity in the phosphodiester backbone between the 3′ hydroxyl of one nucleotide and the 5′ phosphate of the adjacent nucleotide along a DNA strand.
NLS:
See nuclear localization sequence.
NMD:
See nonsense-mediated mRNA decay.
NMR:
See nuclear magnetic resonance spectroscopy.
NOESY:
See nuclear Overhauser effect spectroscopy.
nondisjunction:
The failure of paired chromosomes or sister chromatids to segregate during mitotic or meiotic cell division.
nonhomologous end joining (NHEJ):
A method for repairing double-strand breaks by joining nonhomologous DNA ends in a process that does not conserve the original sequence.
nonpolar:
Hydrophobic; describes molecules or groups that have no effective dipole moment and are therefore poorly soluble in water.
nonsense-mediated mRNA decay (NMD):
A pathway for degradation of mRNA molecules with a premature stop codon, triggered by the presence of an exon junction complex on a transcript that has been translated. Compare non-stop mRNA decay.
nonsense mutation:
A mutation that results in the premature termination of a polypeptide chain.
non-stop mRNA decay:
A pathway for degradation of mRNA molecules lacking a stop codon, triggered by release of the ribosome from the 3′ end of the message. Compare nonsense-mediated mRNA decay.
nontemplate strand:
See coding strand.
Northern blotting:
A nucleic acid hybridization procedure in which one or more specific RNA fragments are detected in a larger population by hybridization to a complementary, labeled DNA probe.
N-terminus (amino terminus):
See amino terminus.
nuclear localization sequence (NLS):
An amino acid sequence that targets a protein for transport to the nucleus.
nuclear magnetic resonance (NMR) spectroscopy:
A technique that utilizes certain quantum mechanical properties of atomic nuclei to study the structure and dynamics of the molecules of which they are a part.
nuclear Overhauser effect spectroscopy (NOESY):
A type of two-dimensional nuclear magnetic resonance spectroscopy in which atoms that are near to one another in space, but not necessarily nearby in the primary structure, can be identified.
nucleases:
Enzymes that hydrolyze the internucleotide (phosphodiester) linkages of nucleic acids.
nucleic acids:
Biologically occurring polynucleotides in which the nucleotide residues are linked in a specific sequence by phosphodiester bonds; DNA and RNA.
nucleoid:
In bacteria, the nuclear zone that contains the chromosome but has no surrounding membrane.
nucleolytic proofreading:
A pathway for the correction of errors in an RNA transcript in which the RNA polymerase reverses direction by one or a few nucleotides on the template, and its endonuclease activity hydrolyzes the phosphodiester backbone of the transcript proximal to the mismatched base.
nucleophile:
An electron-rich group with a strong tendency to donate electrons to an electron-deficient nucleus (electrophile); the entering reactant in a bimolecular substitution reaction.
nucleoside:
A compound consisting of a purine or pyrimidine base covalently linked to a pentose.
nucleosome:
In eukaryotes, the structural unit for packaging chromatin; consists of a DNA strand wound around a histone core.
nucleotide:
A nucleoside phosphorylated at one or more of its pentose hydroxyl groups.
nucleotide excision repair (NER):
A DNA repair pathway that involves excinuclease-catalyzed cleavage of the phosphodiester bond on either side of a bulky DNA lesion such as a pyrimidine dimer or base adduct, followed by removal of the segment containing the lesion, then DNA polymerization and ligation to fill the gap.
Okazaki fragment:
A short segment of DNA synthesized on the lagging strand during DNA replication.
oligomer:
A short polymer, usually of amino acids, sugars, or nucleotides; the definition of “short” is somewhat arbitrary, but usually fewer than 50 subunits.
oligomeric state:
The number of identical polypeptide subunits in a particular form of a protein. For example, monomer, dimer, and trimer are different oligomeric states.
oligonucleotide:
A short polymer of nucleotides (usually fewer than 50).
oligonucleotide-directed mutagenesis:
A method for creating a mutation in a cloned gene. Two short, complementary synthetic DNA strands, each with the desired base change, are annealed to opposite strands of the cloned gene within a suitable vector. The two annealed oligonucleotides prime DNA synthesis, creating two complementary strands with the mutation.
oncogene:
A gene that, when subjected to particular mutations or introduced as part of the genome of particular viruses, causes cells to exhibit rapid, uncontrolled proliferation leading to cancer.
open complex:
(1) A complex of the RNA polymerase bound to a promoter, in which the bound DNA is partially unwound. Transcription initiation occurs in the open complex. Compare closed complex. (2) A complex assembled on the E. coli origin of replication, oriC, at an early stage of replication initiation. It includes an oligomer of the AAA+ protein DnaA, ATP, and the histonelike protein HU.
open form:
The conformation assumed by E. coli DNA polymerase I when a primed template is bound to the active site, but the correct dNTP is not.
open reading frame (ORF):
A group of contiguous nonoverlapping nucleotide codons in a DNA or RNA molecule that does not include a termination codon.
operator:
A region of DNA that interacts with a repressor protein to control the expression of a group of genes organized in an operon.
operon:
A unit of genetic expression consisting of one or more cotranscribed genes and the operator and promoter sequences that regulate their transcription.
optically active:
Able to rotate the plane of plane-polarized light.
ORC:
See origin recognition complex.
ORF:
See open reading frame.
organelles:
Membrane-bounded structures found in eukaryotic cells; contain enzymes and other components required for specialized cell functions.
ori:
See origin of replication.
origin of replication (ori):
The nucleotide sequence or site in DNA where DNA replication is initiated.
origin recognition complex (ORC):
A eukaryotic initiator protein complex that assembles at an origin to initiate replication.
orthologs:
Genes in different organisms that possess a clear sequence and functional relationship to each other. Compare paralogs.
outgroup:
A taxon outside the group of interest in a phylogenetic tree.
pair-rule genes:
A subclass of the segmentation genes expressed in alternate body segments of the developing Drosophila embryo, after the gap genes and before the segment polarity genes.
palindrome:
A segment of duplex DNA in which the base sequences of the two strands exhibit twofold rotational symmetry about an axis.
parallel β sheet:
See β sheet.
paralogs:
Genes within a species that possess a clear sequence and functional relationship to each other and probably arose as the result of a gene duplication. Compare orthologs.
parthenogenesis:
Reproduction by the growth and development of an unfertilized egg.
P body:
See processing body.
PCNA:
Proliferating cell nuclear antigen, the eukaryotic sliding clamp protein that tethers DNA polymerase to the DNA at the replication fork.
PCR:
See polymerase chain reaction.
PDB:
See Protein Data Bank.
peptide bond:
A substituted amide linkage between the α-amino group of one amino acid and the α-carboxyl group of another, with elimination of the elements of water.
peptide prolyl cis-trans isomerase:
An enzyme that catalyzes the interconversion of the cis and trans isomers of proline peptide bonds.
peptide translocation complex:
A complex in the endoplasmic reticulum (ER) that catalyzes the translocation into the ER lumen of a growing polypeptide chain containing an N-terminal signal sequence.
peptidyl transferase reaction:
The reaction that synthesizes the peptide bonds of proteins—nucleophilic attack of the α-amino group of the ribosomal A-site aminoacyl-tRNA on the carbonyl carbon of the ester bond linking the fMet (or the growing peptide chain) to the P-site tRNA. The reaction is catalyzed by a ribozyme, part of the rRNA of the large ribosomal subunit.
P generation:
The parental generation in a genetic cross.
pH:
The negative logarithm of the hydronium ion concentration of an aqueous solution.
phase variation:
The expression of alternative primary cell surface antigens used by some pathogenic bacteria and parasitic protists as a means of eluding a host’s immune system.
phenotype:
The observable characteristics of an organism.
phenotypic function (of a gene product):
The effect of a gene product on the entire organism. Compare cellular function and molecular function.
phosphatases:
Enzymes that hydrolyze a phosphate ester or anhydride, releasing inorganic phosphate, Pi.
phosphodiester bond:
A chemical grouping that contains two alcohols esterified to one molecule of phosphoric acid, which thus serves as a bridge between them.
photoreactivation:
The repair of a cyclobutane pyrimidine dimer by electron transfer from a DNA photolyase.
phylogenetic profiling:
A bioinformatic technique used to discover structure-function relationships by searching for genes that consistently appear together across many genomes.
phylogenetics:
The study of the evolutionary relationships among organisms.
phylogeny:
The evolutionary relationships among organisms.
pi stacking:
The attractive, noncovalent interactions between aromatic rings; important in base stacking in nucleic acids.
pKa:
The negative logarithm of an acid dissociation constant.
plasmid:
An extrachromosomal, independently replicating, small circular DNA molecule; commonly used in genetic engineering.
plectonemic supercoiling:
A structure in a molecular polymer that has a net twisting of strands about each other in some simple and regular way.
pluripotent:
Describes stem cells that can differentiate into cells derived from any of the three germ layers.
pOH:
The negative logarithm of the hydroxyl ion concentration of an aqueous solution.
point mutation:
A mutation consisting of a single base-pair change.
polar covalent:
Describes a type of covalent bond between atoms of different electronegativities, such that the electrons are shared unequally between the atoms.
polar:
Hydrophilic, or “water-loving”; describes molecules or groups that have a dipole moment and are therefore soluble in water.
polarity:
In a developing embryo, the distinct areas that will become the anterior, posterior, dorsal, and ventral parts of the adult organism.
Pol I:
See DNA polymerase I; RNA polymerase I.
Pol II:
See DNA polymerase II; RNA polymerase II.
Pol III:
See DNA polymerase III; RNA polymerase III.
Pol III core:
A complex of the α, ε, and θ subunits of the E. coli DNA polymerase III with polymerase and 5′→3′ proofreading exonuclease activities.
Pol III holoenzyme:
The 17-subunit E. coli DNA polymerase III complex, responsible for chromosomal replication. It includes two Pol III, two sliding clamps, and a clamp-loading complex. Compare RNA polymerase holoenzyme and RNA polymerase III.
poly(A) addition site:
The site where an mRNA is cleaved by a specific endonuclease to generate the free 3′ hydroxyl to which A residues are added. The site is marked by a highly conserved 5′-AAUAAA sequence 10 to 30 nucleotides on the 5′ side, and a G- and U-rich region 20 to 40 nucleotides on the 3′ side.
poly(A) site choice:
The existence of more than one site in an mRNA that may be cleaved to generate the free 3′ hydroxyl to which A residues are added, which can generate diverse transcripts from a single gene.
poly(A) tail:
See 3′ poly(A) tail.
polycistronic mRNA:
A contiguous mRNA with more than two genes that can be translated into proteins.
polyglutamine (polyQ) disease:
A triplet expansion disease caused by the insertion of many additional glutamine codons in a gene. Fragile X syndrome and Huntington disease are polyglutamine diseases.
polylinker:
A short, synthetic fragment of DNA containing recognition sequences for several restriction endonucleases that is inserted into a cloning vector.
polymerase chain reaction (PCR):
A repetitive laboratory procedure that results in a geometric amplification of a specific DNA sequence.
polynucleotide:
A covalently linked sequence of nucleotides in which the 3′ hydroxyl of the pentose of one nucleotide residue is joined by a phosphodiester bond to the 5′ hydroxyl of the pentose of the next residue.
polypeptide chain:
A long chain of amino acids linked by peptide bonds; the molecular weight is generally less than 10,000. Also called a polypeptide.
polyQ disease:
See polyglutamine disease.
polyribosome:
See polysome.
polysome:
A complex of an mRNA molecule and two or more ribosomes. Also called a polyribosome.
positive regulation:
The increased expression of a gene by the binding of an activator protein. Compare negative regulation.
positive supercoiling:
The twisting of a helical (coiled) molecule on itself to form a left-handed supercoil.
postinsertion site:
A site within the active site of a DNA polymerase where the primer 3′-terminal base pair is positioned. Compare insertion site.
posttranslational modification:
The enzymatic processing of a polypeptide chain after translation from its mRNA.
postulate of objectivity:
The only assumption made by scientists—that basic forces and laws in the universe are not subject to change and can thus be studied and defined by scientific inquiry. The term was introduced by Jacques Monod.
precursor miRNA (pre-miRNA):
A partially processed RNA intermediate that is transported from the nucleus to the cytoplasm for final processing into an miRNA by the endonuclease Dicer.
preinitiation complex:
A eukaryotic nucleoprotein complex consisting of intact, double-stranded promoter DNA, Pol II, and various transcription factors. Compare closed complex (in bacteria).
pre-miRNA:
See precursor miRNA.
prepriming complex:
The complex of proteins assembled at oriC in E. coli at an early stage of replication fork assembly. The complex includes a DnaA oligomer bound to the DNA and DnaB helicases stabilizing the single strands of DNA in the replication “bubble.”
preRC:
See prereplication complex.
prereplication complex (preRC):
The complex of proteins, including the origin recognition complex (ORC) and MCMs, that assembles during the G1 phase of the eukaryotic cell cycle, thereby marking the origin for replication during S phase.
preribosomal RNA (pre-rRNA):
The primary transcript of ribosomal RNAs in bacterial and eukaryotic cells, which is processed into mature ribosomal RNAs (and transfer RNAs in bacteria).
pre-rRNA:
See preribosomal RNA.
pre–steady state:
The time immediately after an enzyme is mixed with its substrate, before the free enzyme and its intermediates have reached their steady-state concentrations.
primary miRNA transcript (pri-miRNA):
An RNA transcript that can fold into an extensive hairpin structure, which becomes a substrate for cleavage by the nuclear endonuclease Drosha into a smaller hairpin structure called pre-miRNA.
primary structure:
A description of the covalent backbone of a polymer (macromolecule), including the sequence of monomeric subunits and any interchain and intrachain covalent bonds.
primary transcript:
The immediate RNA product of transcription before any posttranscriptional processing reactions.
primase:
An enzyme that catalyzes the formation of RNA oligonucleotides used as primers by DNA polymerases.
primed template:
A template nucleic acid strand annealed to an RNA or DNA primer.
primer strand:
A strand of nucleic acid with a free 3′-OH group to which a DNA polymerase can add nucleotides.
primer terminus:
The end of a primer to which monomeric subunits are added.
pri-miRNA:
See primary miRNA transcript.
prion:
A misfolded protein in the nervous tissue of mammals that acts as an infectious agent, causing other proteins to misfold and accumulate, leading to the development of spongiform encephalopathy.
probe:
A labeled fragment of nucleic acid containing a nucleotide sequence complementary to a genomic sequence that one wishes to detect in a hybridization experiment.
processing body (P body):
An area in the cytoplasm of a eukaryotic cell where mRNAs that are not being translated are sequestered, possibly for degradation.
processive synthesis:
The enzymatic synthesis of a biological polymer in which the enzyme adds multiple subunits without dissociating from the substrate. Compare distributive synthesis.
processivity:
For any enzyme that catalyzes the synthesis of a biological polymer, the property of adding multiple subunits to the polymer without dissociating from the substrate.
product:
A molecule formed in a chemical reaction.
proenzyme:
A precursor form of an enzyme, before it is cleaved into its active form.
promoter:
A DNA sequence at which RNA polymerase may bind, leading to initiation of transcription.
promoter clearance:
Movement of the transcription complex away from the promoter, which marks the beginning of the elongation stage of transcription.
proofreading:
The correction of errors in the synthesis of an information-containing biopolymer by removing incorrect monomeric subunits after they have been covalently added to the growing polymer.
prophage:
A bacteriophage genome incorporated into the host DNA or as an autonomously replicating plasmid, with most of its genes repressed; a lysogenized bacteriophage genome.
prophage induction:
The process in which a lysogen switches from lysogenic growth to lytic growth.
prophase:
The first stage of mitosis (M phase). Chromosomes duplicated in S phase begin to condense and become visible in the light microscope.
proprotein:
A precursor form of a protein, before it is cleaved into its functional form.
prosthetic group:
A metal ion or an organic compound (other than an amino acid) that is covalently bound to a protein and is essential to its activity.
proteasome:
A large assembly of enzymatic complexes that function in the degradation of damaged or unneeded cellular proteins. In eukaryotes, also called a 26S proteasome.
Protein Data Bank (PDB):
An international database (www.rcsb.org/pdb) that archives data describing the three-dimensional structure of nearly all macromolecules for which structures have been published.
protein disulfide isomerase:
An enzyme that catalyzes the breakage and formation of disulfide cross-links in a protein.
protein family:
A group of evolutionarily related proteins with similar primary sequence and function.
protein folding:
The process by which a polypeptide chain attains its biologically active conformation.
protein kinases:
Enzymes that transfer the terminal phosphoryl group of ATP or another nucleoside triphosphate to a Ser, Thr, Tyr, Asp, or His side chain in a target protein, thereby regulating the activity or other properties of that protein.
protein phosphatases:
Enzymes that hydrolyze a phosphate ester or anhydride on specific amino acid residues of a protein, releasing inorganic phosphate, Pi.
proteolytic cleavage:
The enzyme-catalyzed breakage of peptide bonds in proteins.
proteome:
The full complement of proteins expressed in a given cell under a given set of conditions, or the complete complement of proteins that can be expressed by a given genome.
proteomics:
Broadly, the study of the protein complement of a cell or organism.
protomer:
A general term describing any repeated unit of one or more stably associated protein subunits in a larger protein structure. If a protomer has multiple subunits, the subunits may be identical or different.
P site:
The site in a ribosome occupied by the peptidyl-tRNA.
PUF family:
In eukaryotic cells, a family of proteins that bind the 3′ untranslated region of mRNAs to suppress their translation.
pulsed field gel electrophoresis:
A variation on the technique of gel electrophoresis in which the direction of the current passed through the gel is altered at regular intervals. This allows the separation of larger molecules of DNA than is possible with conventional gel electrophoresis. See also gel electrophoresis.
Punnett square:
A matrix for displaying the genes involved in a cross and the possible combinations of alleles in the progeny. The gamete genotypes are written along the top and sides of the square; the possible combinations of alleles are shown in the matrix.
purebred:
Describes an individual homozygous for a given trait or set of traits.
purine:
A nitrogenous heterocyclic base found in nucleotides and nucleic acids; contains fused pyrimidine and imidazole rings.
puromycin:
An antibiotic that inhibits polypeptide synthesis by being incorporated into a growing polypeptide chain, causing its premature termination.
pyrimidine:
A nitrogenous heterocyclic base found in nucleotides and nucleic acids.
pyrimidine dimer:
A covalently joined dimer of two adjacent pyrimidine residues in DNA, induced by absorption of UV light; most commonly derived from two adjacent thymines (a thymine dimer).
pyrophosphorolysis:
The reverse of a nucleotide polymerization reaction, in which pyrophosphate reacts with the 3′-nucleotide monophosphate of an oligonucleotide, releasing the corresponding nucleotide triphosphate.
pyrosequencing:
A method for rapid DNA sequencing in which nucleotide additions are detected with flashes of light.
qPCR:
See quantitative PCR.
quantitative PCR (qPCR):
A polymerase chain reaction (PCR) protocol that allows the simultaneous amplification and detection of a sequence through use of a fluorescent probe. See also polymerase chain reaction.
quaternary structure:
The three-dimensional structure of a multisubunit protein, particularly the manner in which the subunits fit together.
quorum sensing:
The regulation of gene expression in response to fluctuations in cell population density, assessed by the detection of small, diffusible signaling molecules secreted by the cells.
Rad51:
A eukaryotic recombinase structurally and functionally homologous to the RecA protein of E. coli. See also Dmc1.
Ramachandran plot:
A graphical representation of the ϕ and ψ angles of the amino acid residues in a polypeptide.
rate constant:
The proportionality constant that relates the velocity of a chemical reaction to the concentration(s) of the reactant(s).
rate-limiting step:
(1) Generally, the step in an enzymatic reaction with the greatest activation energy or the transition state of highest free energy. (2) The slowest step in a metabolic pathway.
reactant:
A starting material in a chemical reaction.
reaction intermediate:
Any chemical species in a reaction pathway that has a finite chemical lifetime (greater than a molecular vibration, or 10−13 seconds).
reaction kinetics:
See kinetics.
reaction mechanism:
The sequence of individual steps that take place during the conversion of reactants to products in a chemical reaction.
reading frame:
A contiguous, nonoverlapping set of three-nucleotide codons in DNA or RNA.
RecA protein:
A non-site-specific bacterial recombinase that binds single-stranded DNA and promotes homologous recombination. RecA protein also has co-protease activity in the autocatalytic cleavage of some transcription repressors.
RecBCD:
A bacterial protein complex that prepares DNA at a double-strand break for repair. The complex has helicase activity to unwind the DNA, an endonuclease activity that creates 3′ single-stranded overhangs, and an activity that loads RecA protein on the 3′-ending single strand.
recessive:
Describes an allele that manifests in a homozygous individual but is masked by the dominant allele in heterozygotes. Compare dominant.
RecFOR:
A bacterial recombination mediator that loads RecA protein on single-strand gaps in need of repair.
recognition helix:
The α helix in a DNA regulatory protein that recognizes and binds to the DNA regulatory site.
recognition sequence:
A specific nucleotide sequence in a double-stranded DNA molecule that is recognized by a restriction endonuclease as a substrate.
recombinant:
Any DNA or chromosome in which segments from different sources are combined.
recombinant DNA:
DNA formed by joining DNA molecules, sometimes from different species, in new combinations.
recombinant DNA technology:
Laboratory methods used for genetic engineering.
recombinase:
An enzyme that catalyzes genetic recombination by the reciprocal exchange of short pieces of DNA between longer DNA molecules.
recombination:
(1) The reciprocal exchange of alleles between chromosomes. Also called crossing over. (2) At the molecular level, any enzymatic process by which the linear arrangement of nucleic acid sequences in a chromosome or plasmid is altered by cleavage and rejoining.
recombinational DNA repair:
Recombinational processes directed at the repair of DNA strand breaks or cross-links, especially at inactivated replication forks.
recombination mapping:
The process of determining the relative distance between genes on a chromosome based on the frequency of recombination of alleles during meiosis.
refinement:
In x-ray crystallography, an iterative stage in which the computed diffraction pattern of a predicted model of a three-dimensional structure is compared with the diffraction pattern obtained from the crystal in an experiment.
reflection spot:
In x-ray crystallography, an area on a film or x-ray detector created by the constructive interference of x rays diffracted from the atoms in a unit cell of a crystal.
regulated gene expression:
The conditional expression of a gene based on the cellular need for the gene product, achieved by the presence or absence of activators, repressors, enhancers, and other regulatory factors. Compare constitutive gene expression.
regulatory enzyme:
An enzyme with a regulatory function, through its capacity to undergo a change in catalytic activity by allosteric mechanisms or by covalent modification.
regulatory sequence:
A DNA sequence involved in regulating the expression of a gene; for example, a promoter or operator. Also called a regulatory site.
regulatory site:
See regulatory sequence.
regulon:
A group of genes or operons that are coordinately regulated even though some, or all, may be spatially distant in the chromosome or genome.
relaxed DNA:
Any DNA that exists in its most stable and unstrained structure, typically the B form under most cellular conditions.
release factors:
Protein factors required for the release of a completed polypeptide chain from a ribosome. Also called termination factors. See also RF-1, RF-2, and RF-3.
replicase:
A general term describing any polymerase enzyme that duplicates chromosomes. Also called a chromosomal replicase.
replication factor C (RFC):
The eukaryotic clamp loading complex.
replication fork:
The Y-shaped structure generally found at the point where DNA is being synthesized.
replication protein A (RPA):
A eukaryotic single-stranded DNA-binding protein; its bacterial homolog is SSB.
replicon:
The length of DNA replicated from a single origin.
replisome:
The multiprotein complex that promotes DNA synthesis at the replication fork.
replisome progression complex:
A large protein assemblage that is part of the eukaryotic replication machinery; includes proteins that move with the replication fork, proteins that participate in affixing Pol α in the replisome, and several nonessential proteins thought to control the rate of replication during times of cellular stress.
repression:
A decrease in the expression of a gene in response to a change in the activity of a regulatory protein.
repressor:
A protein that binds to the regulatory sequence or operator for a gene, blocking its transcription.
resonance:
A conceptual view of the delocalized electrons in the bonding structure of a molecule that can only be described as the average of two or more Lewis structures.
resonance hybrid:
A molecule that exists in an average of two possible resonance forms. See also resonance.
restriction endonucleases:
Site-specific endodeoxyribonucleases that cleave both strands of DNA at points in or near the specific site recognized by the enzyme; important tools in genetic engineering.
retrohoming:
The integration of a mobile group II intron into DNA by the reverse splicing of its RNA transcript into a target site (catalyzed by an encoded endonuclease), followed by DNA synthesis (catalyzed by an encoded reverse transcriptase).
retrotransposable element:
See retrotransposon.
retrotransposon (retrotransposable element):
A transposon that moves via an RNA intermediate that is converted back to DNA by reverse transcriptase.
retrovirus:
An RNA virus containing a reverse transcriptase.
reverse transcriptase:
An RNA-directed DNA polymerase in retroviruses; capable of making DNA complementary to an RNA.
reverse transcriptase PCR (RT-PCR):
A polymerase chain reaction (PCR) protocol for amplifying an RNA sequence by first using reverse transcriptase to create a DNA copy. See also polymerase chain reaction and reverse transcriptase.
reverse turn:
A segment of a polypeptide chain in a folded protein or domain that connects two regions of secondary structure with reversed N-to-C directions.
reversible inhibition:
Inhibition by a molecule that binds reversibly to the enzyme, such that the enzyme activity returns when the inhibitor is no longer present.
reversible terminator sequencing:
A method used in many protocols for rapid DNA sequencing.
reversion mutation:
A mutation in a gene that reverses a previous mutation. Also called a back mutation. A true reversion restores the original gene sequence; a second-site reversion restores the functionality (phenotype).
R factor:
The residual error in a model of the three-dimensional structure of a molecule obtained by x-ray crystallography. The R factor is the difference between the calculated diffraction pattern based on the model and the actual diffraction pattern obtained from the crystal.
RFC:
See replication factor C.
RF-1:
A bacterial class I release factor that recognizes the stop codons UAG and UAA and induces peptidyl transferase to transfer the growing polypeptide to water.
RF-3:
A bacterial class II release factor with GTPase activity that catalyzes the dissociation of RF-1 and RF-2 from the ribosome.
RF-2:
A bacterial class I release factor that recognizes the stop codons UGA and UAA and induces peptidyl transferase to transfer the growing polypeptide to water.
R group:
(1) Formally, an abbreviation denoting any alkyl group. (2) Occasionally, used in a more general sense to denote virtually any organic substituent (the R groups of amino acids, for example).
ribonuclease:
A nuclease that catalyzes the hydrolysis of certain internucleotide linkages of RNA.
ribonucleic acid:
See RNA.
ribonucleoprotein (RNP):
A molecular complex of RNA and protein, such as the ribosome.
ribonucleoside 3′-monophosphates:
Metabolites produced during the enzymatic or alkaline hydrolysis of RNA.
ribonucleoside 2′-monophosphates:
Metabolites produced during the enzymatic or alkaline hydrolysis of RNA.
ribonucleoside 2′,3′-cyclic monophosphates:
Metabolites produced during the enzymatic or alkaline hydrolysis of RNA.
ribonucleotide:
A nucleotide containing d-ribose as its pentose component.
ribosomal protein (r-protein):
A protein serving as a component of ribosomes.
ribosomal RNA (rRNA):
A class of RNA molecules serving as components of ribosomes.
ribosome:
A macromolecular complex of rRNAs and r-proteins; the site of protein synthesis.
ribosome binding site:
A sequence in an mRNA that is required for binding bacterial ribosomes. Also called the Shine-Dalgarno sequence.
ribosome recycling:
The disassembly of a translated mRNA, deacylated tRNAs, and ribosomal subunits in preparation for new rounds of translation.
ribosome recycling factor:
A bacterial factor involved in ribosome recycling that binds to the empty ribosomal A site and recruits EF-G to stimulate release of the deacylated tRNAs in the P and E sites.
riboswitch:
A structured segment of an mRNA that binds to a specific ligand and affects the translation or processing of the mRNA.
ribozyme (catalytic RNA):
A ribonucleic acid molecule with catalytic activity; an RNA enzyme.
ricin:
An extremely toxic protein of the castor bean that inactivates the 60S subunit of eukaryotic ribosomes by depurinating a specific adenosine in 23S rRNA.
rifampicin:
An antibiotic that acts as a bacterial transcription inhibitor by binding to the β subunit of bacterial RNA polymerase, preventing promoter clearance.
RISC:
See RNA-induced silencing complex.
RNA (ribonucleic acid):
A polyribonucleotide of a specific sequence linked by successive 3′,5′-phosphodiester bonds.
RNA degradation:
The complete hydrolysis of RNA into its component ribonucleotides, usually catalyzed by ribonucleases or the exosome.
RNA editing:
The posttranscriptional modification of an mRNA that alters one or more codons prior to translation.
RNAi:
See RNA interference.
RNA-induced silencing complex (RISC):
A cytoplasmic complex, including the endonucleases Dicer and Argonaute, that incorporates an miRNA or an siRNA, delivers it to its complementary mRNA target, and then cleaves the mRNA.
RNA interference (RNAi):
Methods of gene silencing, mediated by short interfering RNAs (siRNAs) or microRNAs (miRNAs), which bind to and silence the mRNA transcript, usually by targeting it for degradation. MicroRNAs are endogenous to the cell, produced by nucleases from longer transcripts encoded in the genome; siRNAs are generated by the same cellular enzymes from exogenous double-stranded RNA, introduced into the cell by viral infection or experimental manipulation.
RNA polymerase:
An enzyme that catalyzes the formation of RNA from ribonucleoside 5′-triphosphates, using a strand of DNA as a template. Some RNA polymerases, primarily in viruses, use RNA as a template and are called RNA-dependent RNA polymerases (RDRPs).
RNA polymerase I (Pol I):
One of the three eukaryotic RNA polymerases; Pol I transcribes genes encoding large rRNA precursors.
RNA polymerase II (Pol II):
One of the three eukaryotic RNA polymerases; Pol II transcribes most of the protein-coding genes.
RNA polymerase III (Pol III):
One of the three eukaryotic RNA polymerases; Pol III transcribes genes encoding tRNAs, some snRNAs, 5S ribosomal RNA, and other small functional RNAs.
RNA polymerase core:
The E. coli RNA polymerase complex of subunits α2ββ′ω, exclusive of the σ subunit. Compare Pol III core.
RNA polymerase holoenzyme:
The complete E. coli RNA polymerase complex, including the α2ββ′ω core and the σ subunit. Compare Pol III holoenzyme.
RNA secondary structure:
The local spatial arrangement of an RNA strand, including a description of any intrachain base pairing.
RNaseH:
An endonuclease that cleaves the 3′-O–P bond of RNA in an RNA-DNA duplex.
RNA-Seq:
A strategy for determining the level of expression of all the genes in a cell or tissue by sequencing the transcriptome.
RNA splicing:
The removal of introns and joining of exons in a primary transcript.
RNA world hypothesis:
The hypothesis that in an early stage of evolution, a living system was based on RNA. In this system, RNA enzymes could catalyze the synthesis of all the molecules required for life from simpler molecules available in the environment.
RNP:
See ribonucleoprotein.
Rossmann fold:
A protein supersecondary structure with alternating β strands and α helices (β-α-β-α-β motif), common in nucleotide-binding proteins.
RPA:
See replication protein A.
r-protein:
See ribosomal protein.
RRF:
See ribosome recycling factor.
RT-PCR:
See reverse transcriptase PCR.
Sanger sequencing method:
Refers to two methods developed by Frederick Sanger, (1) for determining the sequence of a polypeptide and (2) for determining the base sequence of a DNA molecule. The DNA sequencing method uses dideoxynucleotides to terminate synthesis; products are analyzed on a gel.
scanning:
The process by which a partially assembled eukaryotic initiation complex slides along the mRNA until it comes to a start codon.
scientific method:
A variety of approaches for generating new knowledge, all focused exclusively on the natural world. In a common variant, a hypothesis is generated, tested, and then strengthened or discarded, depending on the outcome of the test.
scientific theory:
An idea or principle that has been verified in numerous independent experiments over a significant period of time and that is used as the basis for generating new hypotheses.
SCOP database:
See Structural Classification of Proteins (SCOP) database.
screenable marker:
A gene introduced into a cell that allows any colony expressing it to be readily identifiable by its color or fluorescence. Compare selectable marker.
SDSA:
See synthesis-dependent strand annealing.
SDS-PAGE:
See sodium dodecyl sulfate–polyacrylamide gel electrophoresis.
secondary structure:
The local spatial arrangement of the main-chain atoms in a segment of a polypeptide chain; the term is also applied to polynucleotide structure. See also RNA secondary structure.
second law of thermodynamics:
The law stating that, in any chemical or physical process, the entropy of the universe tends to increase.
second messenger:
An effector molecule synthesized in a cell in response to an external signal (first messenger) such as a hormone.
segmentation genes:
A group of genes involved in pattern formation in the Drosophila embryo. Segmentation genes are divided into three subclasses: gap genes, pair-rule genes, and segment polarity genes.
segment polarity genes:
A subclass of the segmentation genes, expressed after the pair-rule genes, that determine the anterior-posterior polarity of the developing Drosophila embryo.
selectable marker:
A gene introduced into a cell that either permits the growth of the cell or kills it under a defined set of conditions. Compare screenable marker.
semiconservative:
Describes a mode of DNA replication in which the daughter duplex has one intact parental strand and one newly synthesized strand.
semidiscontinuous:
Describes a mode of DNA replication in which one strand, the leading strand, is replicated continuously, but the opposite strand, the lagging strand, is replicated in shorter, discontinuous segments.
sequence polymorphisms:
Any alterations in genomic sequence (base-pair changes, insertions, deletions, rearrangements) that help distinguish subsets of individuals in a population or distinguish one species from another.
sequence motif:
Any nucleotide or amino acid sequence that appears in multiple nucleic acids or proteins and has a demonstrable molecular function.
sequence tagged site (STS):
Any known sequence that has been mapped in a chromosome and/or clones derived from it.
sequencing depth:
The number of times, on average, that any given sequence among the targeted genomic sequences appears in the sequencing dataset. For example, sequencing to 100-fold coverage indicates that each targeted sequence is represented an average of 100 times in the dataset.
sex chromosome:
A chromosome that determines the male or female sex of an organism. Compare autosome.
shelterin:
A set of proteins that bind to and protect telomere sequences at the ends of eukaryotic chromosomes.
Shine-Dalgarno sequence:
A sequence in an mRNA that is required for binding bacterial ribosomes. Also called the ribosome binding site (RBS).
short interfering RNA (siRNA):
A short (∼21 to 27 nucleotide) double-stranded RNA with 3′ overhangs, created from exogenous double-stranded RNA by the endonuclease Dicer, that participates in the RNAi gene silencing pathway.
short tandem repeat (STR):
A short (typically 3 to 6 bp) DNA sequence repeated multiple times in tandem at a particular location in a chromosome.
shuttle vector:
A recombinant DNA vector that can be replicated in two or more different host species. See also cloning vector.
sigma factor (σ):
A transient subunit of the bacterial RNA polymerase that directs the enzyme to the promoter. Different sigma factors are specific for different promoters. The core RNA polymerase plus the sigma factor constitutes the RNA polymerase holoenzyme.
signal integration:
The control of gene expression by the net effect of multiple, sometimes conflicting, regulatory signals.
signal recognition particle (SRP):
A protein-RNA complex that recognizes and binds the signal sequence in a nascent polypeptide and delivers the ribosome to a peptide translocation complex in the endoplasmic reticulum.
signal sequence:
An amino acid sequence, often at the amino terminus, that signals the cellular fate or destination of a newly synthesized protein.
silent mutation:
A mutation in a gene that causes no detectable change in the peptide sequence of the gene product.
simple-sequence repeats (SSRs):
Highly repeated, nontranslated segments of DNA in eukaryotic chromosomes, often associated with the centromere and telomere, but not restricted to these regions. Their function is unknown.
single bond:
A bond between two elements that involves two electrons.
single molecule real time (SMRT) sequencing:
A method for rapidly sequencing a long segment of a single strand of DNA.
single nucleotide polymorphism (SNP):
A genomic base-pair change that helps distinguish one species from another or one subset of individuals in a population.
single-stranded DNA–binding protein (SSB):
A bacterial protein that binds single-stranded DNA in a sequence-independent fashion.
siRNA:
See short interfering RNA.
sister chromatid pair:
Duplicate chromosomes, attached at the centromere, produced during the S phase of the eukaryotic cell cycle. Sister chromatids separate into individual chromosomes during anaphase of mitosis or anaphase II of meiosis, when the centromere divides.
site-directed mutagenesis:
A set of methods used to create specific alterations in the sequence of a gene.
site-specific recombination:
A type of genetic recombination that occurs only at specific sequences.
6-4 photoproduct:
A pyrimidine dimer in which the C-6 and C-4 atoms of adjacent pyrimidines are linked.
small nuclear ribonucleoprotein (snRNP):
A protein and snRNA complex, found in the nucleus and a component of the spliceosome.
small nuclear RNA (snRNA):
A class of short, noncoding RNAs, typically 100 to 200 nucleotides long, found in the nucleus and involved in the splicing of eukaryotic mRNAs.
small nucleolar ribonucleoprotein (snoRNP):
A protein and snoRNA complex that guides the modification of rRNAs in the nucleolus.
small nucleolar RNA (snoRNA):
A class of short, noncoding RNAs, generally 60 to 300 nucleotides long, found in the nucleolus and involved in the modification of rRNAs.
SMC proteins:
A family of ATPases that modulate the structure and organization of chromosomes.
snoRNA:
See small nucleolar RNA.
snoRNP:
See small nucleolar ribonucleoprotein.
SNP:
See single nucleotide polymorphism.
snRNA:
See small nuclear RNA.
snRNP:
See small nuclear ribonucleoprotein.
sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE):
A type of electrophoresis used to separate proteins on the basis of size. Proteins in experimental samples are denatured and bound along their length by negatively charged molecules of the detergent SDS, giving them a charge proportional to their length. They move through a gel matrix of cross-linked polyacrylamide under an electric field at a rate proportional to their size. See also gel electrophoresis.
solenoidal supercoiling:
The wrapping of a helical molecule to form a coiled superstructure.
solenoid model:
A model for the arrangement of nucleosomes in the 30 nm filament in which the nucleosome array assumes a spiral shape, with the flat sides of adjacent nucleosomes next to each other. Compare zigzag model.
somatic cells:
All cells in a multicellular organism except the germ-line cells.
SOS response:
In bacteria, a coordinated induction of a variety of genes in response to high levels of DNA damage.
Southern blotting:
A DNA hybridization procedure in which one or more specific DNA fragments are detected in a larger population by hybridization to a complementary, labeled nucleic acid probe.
S phase:
The phase of the cell cycle during which the DNA is replicated. The S phase occurs between the G1 and G2 phases.
spliceosome:
A ribonucleoprotein complex that splices mRNAs in eukaryotic cells.
splice site:
A nucleotide sequence within an intron at the intronexon border, where a primary mRNA transcript may be spliced.
Spo11:
A eukaryotic protein that creates double-strand breaks in DNA to initiate recombination in meiotic prophase I.
spongiform encephalopathies:
Transmissible, progressive neurodegenerative diseases caused by prions.
SRP:
See signal recognition particle.
SSB:
See single-stranded DNA-binding protein.
SSR:
See simple-sequence repeats.
standard (Gibbs) free-energy change (ΔG°):
The free-energy change for a reaction occurring under a set of standard conditions: temperature, 298 K; pressure, 1 atm or 101.3 kPa; and all solutes at 1 M concentration. ΔG′° denotes the standard free-energy change at pH 7.0 in 55.5 M water.
start codon:
See initiation codon.
steady state:
A nonequilibrium state of a system through which matter is flowing and in which all components remain at a constant concentration.
steady-state kinetics:
The study of reaction rates under steady-state conditions. See also steady state.
stem cells:
The cells in multicellular organisms that retain the ability to divide and differentiate into other cell types.
step size:
The average number of subunits over which a motor protein moves for each ATP molecule hydrolyzed.
stereochemistry:
The spatial arrangement of the atoms within a molecule.
stereoisomers:
Compounds that have the same composition and the same order of atomic connections but different molecular arrangements.
sticky ends:
Two DNA ends in the same DNA molecule, or in different molecules, with short, overhanging, single-stranded segments that are complementary to each other, facilitating ligation of the ends.
stop codons:
See termination codons.
STR:
See short tandem repeat.
streptomycin:
An aminoglycoside antibiotic that disrupts or inhibits bacterial protein synthesis. At low concentrations it causes misreading of the genetic code; at higher concentrations it inhibits translation initiation by preventing fMet-tRNAfMet from binding to the ribosome.
stringent factor:
A bacterial protein (RelA) recruited to a ribosome when an uncharged tRNA binds. Stringent factor catalyzes the formation of guanosine tetraphosphate (ppGpp), which binds RNA polymerase, reducing transcription from rRNA and tRNA genes and increasing transcription from biosynthetic genes.
stringent response:
A mechanism for coordinating transcriptional activity in bacteria with the levels of amino acids available in the cell. Triggered by the binding of uncharged tRNAs to the ribosome, the stringent response directs the cellular machinery toward amino acid synthesis rather than growth and reproduction.
Structural Classification of Proteins (SCOP) database:
A database (http://scop.berkeley.edu) of the structural and evolutionary relationships among all proteins for which the structures are known.
structural motif:
Any distinct folding pattern for elements of secondary structure, observed in one or more proteins. A motif can be simple or complex and can represent all or just a small part of a polypeptide chain. Also called a fold or a supersecondary structure.
STS:
See sequence-tagged site.
substrate:
A molecule that undergoes an enzyme-catalyzed reaction.
supercoiled DNA:
DNA that twists upon itself because it is underwound or overwound (and thereby strained) relative to B-form DNA.
superfamily:
A structural classification that includes protein families with little sequence similarity but with the same supersecondary structural motif and functional similarities.
superhelical density (σ):
In a helical molecule such as DNA, the number of supercoils (superhelical turns) relative to the number of coils (turns) in the relaxed molecule.
supersecondary structure:
See structural motif.
suppressor tRNA:
A mutant tRNA that binds to a termination codon but carries an amino acyl residue that can be incorporated into the growing amino acid chain, suppressing the termination signal.
surroundings:
All matter in the universe that is outside the system being considered. See also system.
synteny:
Conserved gene order along the chromosomes of different species.
synthesis-dependent strand annealing (SDSA):
A pathway for repairing double-strand breaks that ends with the invading strands dissociating and reannealing and with the homologous DNA molecule intact. See also double-strand break repair.
system:
An isolated collection of matter; all other matter in the universe apart from the system is called the surroundings. See also surroundings.
systems biology:
In biochemistry or molecular biology, the study of complex systems, integrating the functions of the macromolecules in a cell (RNA, DNA, proteins).
tag:
A peptide or protein that binds a simple, stable ligand with high affinity and specificity.
tandem affinity purification (TAP) tags:
Two tags (such as Protein A and calmodulin-binding peptide) fused to the same target protein to allow sequential, highly specific affinity purification steps of the expressed protein.
tandem MS:
Two mass spectrometry procedures carried out in succession to define the mass of peptides generated by proteolytic cleavage of a protein.
TAP tags:
See tandem affinity purification tags.
target-primed (TP) retrotransposon:
A retrotransposon that moves via a cDNA copy of its mRNA transcript and is synthesized as a direct extension of the 3′ end created in the target site by a retrotransposon-encoded endonuclease. See also extrachromosomally primed (EP) retrotransposon.
target site:
The location on a chromosome where a transposon inserts itself. Compare donor site.
TATA-binding protein (TBP):
A eukaryotic transcription factor that binds all three RNA polymerases as well as the AT-rich region of many promoters known as the TATA box.
τ (tau) complex:
A complex of four different proteins that functions in bacteria to load the processivity clamp onto DNA in the bacterial replisome.
taxon:
A grouping of organisms in a phylogenetic tree.
TBP:
See TATA-binding protein.
TCR:
See transcription-coupled repair.
telomerase:
A ribonucleoprotein enzyme that has reverse transcriptase activity and a short RNA sequence that primes the addition of nucleotide repeats to the 3′ ends of DNA. Telomerase activity ensures that no unique sequence information is lost as a result of the end replication problem.
telomerase reverse transcriptase (TERT):
The protein component of telomerase.
telomerase RNA (TR):
The RNA component of telomerase.
telomere:
A specialized nucleic acid structure found at the ends of linear eukaryotic chromosomes.
telomere loop:
See t-loop.
telophase:
The final stage of mitosis (M phase), in which the two sets of homologous chromosomes reach opposite spindle poles and begin to decondense. The cell physically divides in the process of cytokinesis, resulting in two daughter cells.
template strand:
A strand of nucleic acid used by a polymerase as a template to synthesize a complementary strand.
termination:
(1) The third of three stages of RNA synthesis, in which the RNA polymerase and the RNA product are released from the DNA template. (2) The third of three stages of protein synthesis, in which the ribosome and the peptide product are released from the mRNA template.
termination codons:
UAA, UAG, and UGA; in protein synthesis, these codons signal the termination of a polypeptide chain. Also called stop codons.
termination factors:
See release factors.
termination sequence:
A DNA sequence, at the end of a transcriptional unit, that signals the end of transcription.
terminator:
Broadly, a place where transcription is halted. This can occur at the end of a gene (where some termination sequences are also called terminators) or in regulatory sequences preceding some operons (as occurs in transcription attenuation). See also termination sequence.
Ter site:
A 23 bp sequence that serves as a DNA replication termination site in E. coli.
TERT:
See telomerase reverse transcriptase.
tertiary structure:
The three-dimensional conformation of a polymer in its native folded state.
testcross:
Genetic cross of an F1 hybrid with a homozygous recessive strain to determine the genotype of the F1 individual. A testcross also reveals linked genes.
tetracyclines:
A family of antibiotics that inhibit bacterial protein synthesis by occupying the ribosomal A site, thereby preventing the binding of aminoacyl-tRNAs.
tetrad:
A structure formed in meiotic prophase I by the association of two homologous sister chromatid pairs.
thin-layer chromatography:
A process in which complex mixtures of molecules are separated by many repeated partitionings between a flowing (mobile) phase and a stationary phase coated onto a planar surface. Molecules separate based on the rate of their migration across the stationary phase as the mobile phase is drawn through it by capillary action.
30 nm filament:
A higher-order organization of nucleosomes seen in condensed chromosomes.
3′ cleavage:
The cleavage of nascent mRNA molecules in eukaryotes, prior to the addition of poly(A) tails.
3′ poly(A) tail:
A length of adenosine residues (typically 80 to 250) added to the 3′ end of many mRNAs in eukaryotes (and sometimes in bacteria), which serves as a binding site for proteins that protect the mRNA from exonucleases.
thymine (T):
A pyrimidine base that is a component of DNA, but not RNA.
t-loop (telomere loop):
A looped structure seen in mammalian telomeres, in which the single-stranded 3′ end of the chromosome folds back and hybridizes to a duplex portion of the telomere.
TLS:
See translesion synthesis.
tmRNA:
A bacterial RNA that has the properties of a tRNA at its 5′ end and the properties of an mRNA, including a stop codon, at its 3′ end. When aminoacylated, the 5′ end can bind in the A site of a ribosome stalled on a truncated mRNA, and the 3′ end can serve as a template for continued translation through a termination codon that recruits the termination factors required for proper termination and ribosome recycling. Also called transfer-messenger RNA.
topoisomerase:
An enzyme that catalyzes alterations in DNA topology, introducing and/or removing positive or negative supercoils in closed, circular duplex DNA.
topoisomers:
Different forms of a covalently closed, circular DNA molecule that differ only in their linking number.
totipotent:
Describes stem cells from the first few divisions of the fertilized egg that can differentiate into a complete, viable organism.
transcription:
The enzymatic process whereby the genetic information contained in one strand of DNA is used to specify a complementary sequence of bases in an RNA strand.
transcriptional ground state:
The inherent activity of promoters and transcription machinery in vivo in the absence of regulatory mechanisms.
transcription attenuation:
A process for the regulation of expression of a bacterial operon in which transcription begins but is halted before transcription of the operon genes.
transcription-coupled repair (TCR):
A nucleotide excision repair pathway in eukaryotes that is triggered when RNA polymerase encounters a lesion in the DNA and stalls.
transcription factor:
In eukaryotes, a protein that affects the regulation and transcription initiation of a gene by binding to a regulatory sequence near or within the gene and interacting with RNA polymerase and/or other transcription factors.
transcriptome:
The entire complement of RNA transcripts present in a given cell or tissue under specific conditions.
transcriptomics:
The study of transcriptomes.
transfection:
Incorporation of exogenous DNA into a eukaryotic cellular genome by any of several methods.
transfer-messenger RNA:
See tmRNA.
transfer RNA (tRNA):
A class of RNA molecules (Mr 25,000 to 30,000), each of which combines covalently with a specific amino acid for use in protein synthesis.
transformation:
(1) Introduction of an exogenous DNA into a bacterial cell, causing the cell to acquire a new phenotype. (2) The conversion of a cell in a multicellular eukaryote into a cancer cell.
transition mutation:
A point mutation resulting in the exchange of one purine-pyrimidine base pair for another purine-pyrimidine pair. Compare transversion mutation.
transition state:
An activated form of a molecule in which the molecule has undergone a partial chemical reaction; the highest point on the reaction coordinate.
translation:
The process in which the genetic information present in an mRNA molecule specifies the sequence of amino acids during protein synthesis.
translational repressor:
A repressor that binds to an mRNA, blocking translation.
translesion synthesis (TLS):
A pathway for replicating DNA across lesions that occur in unwound DNA at the replication fork. The pathway uses a TLS polymerase that lacks a proofreading exonuclease and has a less-selective active site. Although this polymerase may introduce a mutation, it allows replication to proceed.
translocase:
(1) An enzyme that catalyzes membrane transport. (2) An enzyme that causes movement, such as movement along a double-stranded nucleic acid or the movement of a ribosome along an mRNA.
translocation:
(1) Enzyme-catalyzed movement across a membrane. (2) Movement along a double-stranded nucleic acid without strand separation. (3) Movement of a ribosome by one codon along the mRNA.
translocation mutation:
A mutation that results from the exchange of large segments of DNA between nonhomologous chromosomes.
transposable element:
See transposon.
transposases:
Transposon-encoded enzymes that catalyze the reactions required for the transposon to excise itself from the donor site and insert itself into the target site. These reactions typically include hydrolysis of a specific phosphodiester bond and transesterification involving attack of the liberated 3′ hydroxyl on another phosphodiester bond.
transposition:
The movement of a gene or set of genes from one site in the genome to another.
transposon (transposable element):
A segment of DNA that can move from one position in the genome to another.
trans-splicing:
A process in nematode worms in which a short leader sequence is spliced to the 5′ end of a primary transcript from a separate RNA molecule.
transversion mutation:
A point mutation resulting in the exchange of a purine-pyrimidine base pair for a pyrimidine-purine pair, or vice versa. Compare transition mutation.
triplet expansion disease:
A disease caused by the insertion of many additional copies of a repeated codon triplet into a gene due to template slippage in the DNA replication process.
triplex DNA:
A DNA structure involving three polynucleotide strands bonded through non-Watson-Crick interactions called Hoogsteen pairings.
tRNA-charging step:
The second step in the attachment of an amino acid to a tRNA, in which the aminoacyl-tRNA synthetase transfers the bound aminoacyl-AMP to the 2′-OH or 3′-OH of the 3′-terminal adenosine residue of the tRNA. See also adenylylation step.
trombone model:
A description of DNA replication on the lagging strand, with its repeated cycles of loop growth and disassembly, by analogy with the movement of a slide on a trombone.
tumor suppressor genes:
A class of genes that encode proteins that normally suppress the division of cells. When defective, the normal gene becomes a tumor suppressor gene, and when both copies are defective, the cell is allowed to continue dividing without limitation; it becomes a tumor cell.
tunicamycin:
An antibiotic that inhibits the N-glycosylation of proteins in eukaryotic cells.
turnover number:
The number of times an enzyme molecule transforms a substrate molecule per unit time, under conditions giving maximal activity at substrate concentrations that are saturating. See also general rate constant.
26S proteasome:
In eukaryotes, a large assembly of enzymatic complexes that function in the degradation of damaged or unneeded cellular proteins.
twist (Tw):
The net number of helical turns in a DNA molecule. Compare writhe (Wr).
two-dimensional gel electrophoresis:
A technique that separates the components of a sample on the basis of two properties, in successive steps. For example, a protein sample may be separated on the basis of isoelectric point in one dimension, followed by separation on the basis of relative molecular mass in the other dimension.
two-dimensional NMR:
A type of nuclear magnetic resonance spectroscopy in which different pulses of an electromagnetic field provide two qualitatively distinct signals.
type II restriction endonucleases:
Enzymes that cleave DNA at a specific site within a short recognition sequence, with no requirement for a nucleotide triphosphate cofactor.
type I topoisomerase:
An enzyme that introduces positive or negative supercoils in closed, circular duplex DNA by cleaving one of the two DNA strands, passing the intact strand through the break, and ligating the broken ends. Type I topoisomerases change Lk in increments of 1.
type II topoisomerase:
An enzyme that introduces positive or negative supercoils in closed, circular duplex DNA by cleaving both DNA strands, passing an intact segment of DNA through the break, then religating the broken ends. Type II topoisomerases change Lk in increments of 2.
UAS:
See upstream activator sequence.
uncompetitive inhibitor:
An inhibitor molecule that can bind to the enzyme-substrate complex but not to the free enzyme.
unipotent:
Describes mammalian cells that can reproduce to form more of the same kind of differentiated cell.
unit cell:
The smallest regularly repeating unit in a crystal.
unwinding:
The separation of paired strands of a nucleic acid.
uORF:
See upstream open reading frame.
UP element:
See upstream promoter element.
upstream activator sequence (UAS):
A regulatory sequence in yeast DNA to which transcription activators bind. See also enhancer.
upstream open reading frame (uORF):
A short open reading frame upstream of a gene’s start codon that serves as a decoy to divert ribosomes, thereby down-regulating expression.
upstream promoter (UP) element:
An AT-rich sequence between positions 240 and 260 in the promoters of some highly expressed bacterial genes. The sequence is bound by an α subunit of RNA polymerase, improving the efficiency of transcription initiation for that gene.
uracil (U):
A pyrimidine base that is a component of RNA but not DNA.
valence:
The number of covalent bonds formed by atoms of a particular element.
valence bond model:
A model that proposes that chemical bonds form when half-filled valence atomic orbitals from two atoms overlap.
van der Waals interactions:
Weak intermolecular forces between molecules as a result of each molecule inducing polarization in the other.
van der Waals radius:
Half the distance between two atoms of an element that are as close to each other as possible without being formally bonded. The van der Waals radius defines an imaginary sphere that represents the size of an atom in models.
Vmax:
The maximum velocity of an enzymatic reaction when the binding site is saturated with substrate.
V0:
See initial velocity.
weak chemical bonds:
Chemical interactions such as van der Waals interactions, hydrophobic interactions, and hydrogen bonds that are weaker than formal ionic or covalent bonds.
Western blotting:
A technique that uses antibodies to detect the presence of a protein in a biological sample, after the proteins from the sample have been separated in a gel. Also called immunoblotting.
whole-genome shotgun sequencing:
A strategy for sequencing a genome in which random segments of DNA are sequenced and the segments are ordered by the computerized identification of sequence overlaps.
wild type:
The allele or phenotype that appears with the greatest frequency in a natural population of a species.
Wnt-class signaling pathway:
A type of cell-cell signaling during development that does not require cell-cell contact. Wnt-class genes and proteins are involved in the synthesis, secretion, and reception of glycoprotein signals in developing embryos.
wobble base:
The base at the 5′ end of an anticodon, which pairs loosely and can form mispairs with the base at the 3′ end of the codon.
wobble hypothesis:
A hypothesis proposed by Francis Crick in 1966 to describe how some anticodons can recognize more than one codon.
wobble position:
The first position of the anticodon, at the 5′ end, which may contain a wobble base.
writhe (Wr):
The net number of supercoils in a DNA molecule. Compare twist (Tw).
X chromosome inactivation:
A method of dosage compensation in mammals that involves inactivating one of the two X chromosomes in females by compacting it into heterochromatin.
XIC:
See X inactivation center.
X inactivation center (XIC):
A point on the mammalian X chromosome that is the nucleation center for heterochromatin formation when the chromosome is inactivated.
x-ray crystallography:
The analysis of x-ray diffraction patterns of a crystalline compound, used to determine the molecule’s three-dimensional structure.
YAC:
See yeast artificial chromosome.
yeast artificial chromosome (YAC):
An expression vector for cloning eukaryotic genes in yeast. YAC vectors have a yeast origin of replication, two selectable markers, and telomere and centromere sequences for maintaining chromosome integrity.
yeast three-hybrid analysis:
A method for defining protein-RNA interactions in vivo. A series of engineered proteins and a randomized library of RNA sequences are set up such that expression of a reported gene occurs only when the RNA sequence bound by the target protein is present.
yeast two-hybrid analysis:
A method for defining protein-protein interactions. Target protein interaction activates transcription of a reporter gene.
Z-DNA (Z-form DNA):
A conformation of double-stranded DNA observed in solvents with a high salt concentration or with sequences rich in G≡C base pairs. The molecule assumes a left-handed helical conformation with 12 base pairs per turn and a rise of 3.7 Å per base pair. The backbone of the helix has a zigzag structure. Compare A-DNA and B-DNA.
zigzag model:
A model for the arrangement of nucleosomes in the 30 nm filament in which zigzag histone pairs stack on each other and twist about a central axis. Compare solenoid model.
zinc finger motif:
A protein structural motif involved in DNA recognition by some DNA-binding proteins; characterized by a single atom of zinc coordinated to four Cys residues or to two His and two Cys residues.